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Cláudio M. Soares studied Biochemistry at Universidade de Lisboa, Portugal, where he obtained his first degree in 1989. In 1990 he went to Uppsala University, Sweden where he developed the research that led to his PhD (presented in the University of Lisbon in 1994). After the PhD he joined ITQB NOVA in 1994 and in 1999 he created and start leading the Protein Modelling Laboratory, one of the first labs in Portugal to work in this field. The Protein Modeling Laboratory, founded in 1999, employs computational biophysical and AI methods to investigate the molecular structure and dynamics of proteins. The interaction with experimental laboratories is essential for our current research, which is primarily focused on the design of non-conventional biologicals to combat viral infection and engineering enzymes for the production of high-value compounds. He is co-author of 134 published or accepted papers in peer-reviewed scientific journals and has an h-index of 42 (Scopus; 49 in Google Scholar). He participated in 38 competitively funded projects since 1996 (including 10 international projects, being the coordinator of 5 of these). He was co-author of 104 invited presentations in meetings and institutions. He has supervised 5 Diploma students, 7 master students, 15 research students, 16 PhD students and 13 post-doctoral fellows. His present lab is composed of one Assistant Researcher, 1 Project Manager, 8 PhD students, 3 Research Fellows and 6 master students. He is 1st Secretary of the General Assembly of the Port. Biophys. Soc., and was Chairman of the Port. Biophys. Soc. (2002-2008). He was President of the Fiscal Committee of the Portuguese Biochemical Society (2019-2022), President of the General Assembly of the Portuguese Biochemical Society (2017-2018), member of the International Union for Pure and Applied Biophysics (IUPAB) council (2011-2017), and member of the Federation of European Biochemical Societies (FEBS) Advanced Courses Committee (2015-2018). He is member of the Scientific Council of TAGUSPARK - Parque de Ciência e Tecnologia, Portugal, since 2013 and is President of this Council since 2020. He is Full Professor of Biochemistry since 2022. He was Pro-Rector for the NOVA Health Platform from 2023 to 2025. Cláudio M. Soares was Dean of ITQB NOVA from 2013 to 2023 and was Vice-Dean during the 2005-2008 and 2011-2013 periods. He is Coordinator of the Molecular, Structural and Cellular Microbiology - MOSTMICRO-ITQB Research Unit (evaluated as Excellent) of ITQB NOVA since 2015. He has been in the organisation or in the scientific committee of 30 national and international meetings and acted as Chair in 30 symposia. He has done extensive evaluation work for Research financing agencies from Portugal (Chair in 2016-2018), European Commission, Argentina, Czech Republic (Co-Chair in 2020, 2021 and 2022; Chair in 2024), The Netherlands, USA, Germany, Austria, Cyprus, Poland (Chair in 2024), Romania, Israel. He is Member the Editorial Boards of Scientific Journals i) Biophysical Reviews - From 2011-2021. ii) PLOS One - From 2012 to the present day. iii) Scientific Reports - From 2013 to the present day. iv) FEBS Open Bio - From 2018 to the present day.
Identificação

Identificação pessoal

Nome completo
Claudio Manuel Simões Loureiro Nunes Soares

Nomes de citação

  • Soares, Claudio M.

Identificadores de autor

Ciência ID
DE12-5674-E511
ORCID iD
0000-0003-1154-556X

Endereços de correio eletrónico

  • claudio@itqb.unl.pt (Profissional)

Telefones

Telefone
  • 214469734 (Profissional)

Moradas

  • Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa. Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República – EAN,, 2780-157, Oeiras, Oeiras, Portugal (Profissional)

Websites

Domínios de atuação

  • Ciências Naturais - Ciências Biológicas - Bioquímica
  • Ciências Naturais - Ciências Biológicas - Biofísica
  • Ciências Exatas - Ciências da Computação e da Informação - Bioinformática

Idiomas

Idioma Conversação Leitura Escrita Compreensão Peer-review
Português Utilizador proficiente (C1) Utilizador proficiente (C1) Utilizador proficiente (C1) Utilizador proficiente (C1)
Inglês Utilizador proficiente (C1) Utilizador proficiente (C1) Utilizador proficiente (C1) Utilizador proficiente (C1)
Espanhol; Castelhano Utilizador independente (B1) Utilizador independente (B1) Utilizador elementar (A1) Utilizador independente (B1)
Sueco Utilizador elementar (A1) Utilizador elementar (A1) Utilizador elementar (A1) Utilizador elementar (A1)
Francês Utilizador elementar (A1) Utilizador independente (B1) Utilizador elementar (A1) Utilizador elementar (A1)
Formação
Grau Classificação
2021/05/25 - 2021/05/25
Concluído
Biociências Moleculares (Título de Agregado)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
1990/11/01 - 1994/10/03
Concluído
Bioquímica Teórica (Doutoramento)
Universidade de Lisboa Faculdade de Ciências, Portugal
"Molecular dynamics simulation studies of porin from Rhodobacter capsulatus. Structural aspects and mechanism for pore closure" (TESE/DISSERTAÇÃO)
With honours
1994
Concluído
Filosofie Licentiatexamen (a Swedish degree higher than Master) (Outros)
Uppsala Universitet, Suécia
Without classification
1986/09/01 - 1989/09/30
Concluído
Bioquímica (Licenciatura)
Universidade de Lisboa Faculdade de Ciências, Portugal
"Estudos sobre aldeído desidrogenases de fígado de rato" (TESE/DISSERTAÇÃO)
17 (in a scale of 20)
Percurso profissional

Docência no Ensino Superior

Categoria Profissional
Instituição de acolhimento
Empregador
2022/04/01 - Atual Professor Catedrático (Docente Universitário) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2005/03/01 - 2022/03/31 Professor Associado (Docente Universitário) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
1999/02/01 - 2005/02/28 Professor Auxiliar Convidado (Docente Universitário) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Cargos e Funções

Categoria Profissional
Instituição de acolhimento
Empregador
2020/06/01 - Atual President of the Scientific Council TAGUSPARK – Parque de Ciência e Tecnologia, Portugal
2016/10/01 - Atual Member of European Science Foundation (ESF) College of Expert Reviewers European Science Foundation, França
2023/05/01 - 2025/10/06 Pró-Reitor Universidade Nova de Lisboa, Portugal
Universidade Nova de Lisboa, Portugal
2013/03 - 2023/04/30 Presidente do Conselho Científico Universidade Nova de Lisboa, Portugal
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2013/03 - 2023/04/30 Presidente do Conselho Pedagógico Universidade Nova de Lisboa, Portugal
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2019/01/01 - 2022/12/31 President of the Fiscal Committee Sociedade Portuguesa de Bioquímica, Portugal
2013/05/31 - 2020/05/30 Member of the Scientific Council TAGUSPARK – Parque de Ciência e Tecnologia, Portugal
2010/01/01 - 2013/04/30 ITQB representative in the Teaching Quality System Universidade Nova de Lisboa, Portugal
2009/05/01 - 2010/03/31 Member of the Scientific Council Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2009/05/01 - 2010/03/31 Member of the Institute Council Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2009/05/01 - 2010/03/31 Member of the Pedagogical Council Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2003/01/01 - 2008/12/31 Member of the Scientific Advisory Council Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
1999/01/01 - 2002/12/31 Member of the Co-ordinating Committee of the Scientific Council Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Outros

Categoria Profissional
Instituição de acolhimento
Empregador
2015/01/01 - Atual Coordinator Molecular, Structural and Cellular Microbiology – MOSTMICRO Research Unit of ITQB NOVA, Portugal
2008/11/01 - Atual First Secretary of the General Assembly Sociedade Portuguesa de Biofísica, Portugal
1999/02/01 - Atual Leader of the Protein Modelling Laboratory Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2013/03/01 - 2023/04/30 Dean Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2017/01/01 - 2018/12/31 President of the General Assembly Sociedade Portuguesa de Bioquímica, Portugal
2015/01/01 - 2018/12/31 Member of the FEBS (Federation of European Biochemical Societies) Advanced Courses Committee. Federation of European Biochemical Societies, Reino Unido
2007/01/01 - 2017/12/29 Responsible at ITQB for the MIT-Portugal collaboration program. Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2011/11/01 - 2017/07/31 Member of the Council of the International Union for Pure and Applied Biophysics (IUPAB) International Union for Pure and Applied Biophysics, Reino Unido
2013/01/01 - 2016/12/31 General Secretary of the General Assembly Sociedade Portuguesa de Bioquímica, Portugal
2011/03/01 - 2013/02/28 Vice-Dean Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2007/01/01 - 2012/12 Deputy Director of the PhD Program in Computational Biology Instituto Gulbenkian de Ciência, Portugal
2009/05/01 - 2010/03/31 Head of the Biological Chemistry Division Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2002/12/01 - 2008/10/31 Chairman of the Portuguese Biophysical Society Sociedade Portuguesa de Biofísica, Portugal
2005/06/01 - 2008/02/29 Vice-Dean Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
1994/11/01 - 1999/01/31 Post-doc Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
1990/11/01 - 1994/04/30 PhD student Uppsala Universitet, Suécia
1988/10/01 - 1989/09/30 Diploma student Universidade de Lisboa Faculdade de Ciências, Portugal
Projetos

Bolsa

Designação Financiadores
2024/01/01 - Atual Small biologics discovery: unlocking new antivirals for pandemic preparedness - ID 2023.00583.BD
2023.00583.BD
École Polytechnique Fédérale de Lausanne, Suiça

Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica António Xavier, Portugal
Fundação para a Ciência e a Tecnologia
Em curso
2025/01 - 2029/12 MOLECULAR STRATEGIES AGAINST VIRAL ENTRY AND GLYCAN SHIELDING European Commission
2022/11 - 2025/10 The BioPlaTTAR Platform for the Tailored and Rapid Development of Antiviral Biopharmaceuticals
HR22-00722
Caixabank SA
2016/01 - 2018/12 Engineering a highly active NiFeSe Hydrogenase for electrocatalytic and photocatalytic applications Fundação para a Ciência e a Tecnologia
2016/01 - 2016 Probing the pH-induced conformational change of influenza hamaggglutinin using micro-second long simulations
2010PA3220
Investigador responsável
Partnership for Advanced Computing In Europe
Em curso
2013/03 - 2015/03 Structural Determinants of Oxygen Tolerance in a NiFeSe Hydrogenase Fundação para a Ciência e a Tecnologia, I.P.
2009/06 - 2012/12 Structural and functional study of the proteins mediating electron transfer between microorganisms and solid substrates with relevance for bio-energy production Fundação para a Ciência e a Tecnologia, I.P.
2007/01 - 2008/12 Rationalization of cutinase enantioselectivity in nonaqueous media Fundação para a Ciência e a Tecnologia, I.P.

Projeto

Designação Financiadores
2023/09/01 - Atual Life Sciences for a Healthy and Sustainable Future
LA/P/0087/2020
Universidade Nova de Lisboa Molecular Structural and Cellular Microbiology, Portugal

Universidade Nova de Lisboa, Portugal

GREEN-IT, Portugal

Instituto Gulbenkian de Ciência, Portugal

Instituto de Biologia Experimental e Tecnológica, Portugal

Universidade de Lisboa Centro de Estudos Comparatistas, Portugal

Universidade de Trás-os-Montes e Alto Douro Centro de Investigação e de Tecnologias Agro-Ambientais e Biologicas, Portugal

Instituto Português de Oncologia de Lisboa Francisco Gentil EPE, Portugal
Fundação para a Ciência e a Tecnologia
Em curso
2021/01/01 - Atual PI3K / AKT / mTOR pathway modulation as target therapy in the treatment of breast and colorectal cancer
2019.00199.CBM
Investigador responsável
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
Fundação para a Ciência e a Tecnologia
Em curso
2020/12/01 - Atual Design of protein chimeras targeting SARS-CoV-2
FCT/CPCA/A0/7305/2020
Investigador
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
Fundação para a Ciência e a Tecnologia
Em curso
2020/12 - Atual Design of protein chimeras targeting SARS-CoV-2
FCT/CPCA/A0/7305/2020
Fundação para a Ciência e a Tecnologia
2020/07/01 - Atual A practical assay for routine detection of neutralizing antibodies against SARSCoV2 that bypasses requirements for high biosafety laboratory usage
613719605
Investigador
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
Fundação para a Ciência e a Tecnologia
Em curso
2020/06/01 - Atual Predicting SARS-CoV-2 susceptibility by tracking the genetic variability of the ACE2 receptor
613747728
Investigador
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
Fundação para a Ciência e a Tecnologia
Em curso
2024/01 - 2028/12 EvaMobs - Evolvable and rapidly adaptable monobodies: a broad-spectrum antiviral platform
Horizon Europe HORIZON-HLTH-2023-DISEASE-03 Project 101137419
HORIZON EUROPE Health
2024/09/01 - 2025/04/30 Exploring structural dynamics of viral fusion proteins using Molecular Dynamics simulations
2024.06988.CPCA.A1,
Universidade do Minho Advanced Computing Center, Portugal

Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica António Xavier, Portugal
Fundação para a Ciência e a Tecnologia

Rede Nacional de Computação Avançada
Em curso
2019/01 - 2022/12 Using computational and experimental methods to provide a global characterization of viral fusion peptides
PTDC/CCI-BIO/28200/2017
Investigador responsável
Fundação para a Ciência e a Tecnologia
Em curso
2019 - 2022 SHIKIFACTORY100 - Modular cell factories for the production of 100 compounds from the shikimate pathway
H2020-NMBP-BIO-2018
Investigador responsável
Em curso
2016/01 - 2018/12 Engineering a highly active NiFeSe Hydrogenase for electrocatalytic and photocatalytic applications
PTDC/BBB-BEP/2885/2014
Investigador responsável
Fundação para a Ciência e a Tecnologia
2016/01 - 2018/12 Engineering a highly active NiFeSe Hydrogenase for electrocatalytic and photocatalytic applications
PTDC/BBB-BEP/2885/2014
Fundação para a Ciência e a Tecnologia
2017/01 - 2017/12 Characterization of maltose translocation in the MalFGK2E transporter
Proposal 2010PA4247
Investigador responsável
Partnership for Advanced Computing In Europe
2015/01 - 2017/12 Molecular, Structural and Cellular Microbiology Fundação para a Ciência e a Tecnologia
2014/01 - 2015/12 Incentive - LA 4 - 2014 Fundação para a Ciência e a Tecnologia
2013/03 - 2014 Structural Determinants of Oxygen Tolerance in a NiFeSe Hydrogenase
PTDC/BBB-BEP/0934/2012
Investigador responsável
Fundação para a Ciência e a Tecnologia, I.P.
Concluído
2013/03 - 2014 Structural Determinants of Oxygen Tolerance in a NiFeSe Hydrogenase
PTDC/BBB-BEP/0934/2012
Fundação para a Ciência e a Tecnologia, I.P.
2011 - 2014 Interaction of proteins with CO releasing molecules (CORMS)
PTDC/QUI-BIQ/117799/2010
Investigador responsável
Concluído
2010 - 2014 Membrane fusion mechanism of Influenza Hemagglutinin: a simulation and biophysical approach.
Investigador responsável
Fundação para a Ciência e a Tecnologia, I.P.
Concluído
2010 - 2014 Proton transfer and proton pumping in haem-copper oxidases. Methodological developments and their application to unravel the molecular mechanism.
Investigador responsável
Fundação para a Ciência e a Tecnologia, I.P.
Concluído
2011/01/01 - 2012/12/31 Strategic Project - LA 4 - 2011-2012
PEst-OE/EQB/LA0004/2011
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica António Xavier, Portugal

Universidade Nova de Lisboa Medical School, Portugal

Fundação Calouste Gulbenkian, Portugal

Instituto de Biologia Experimental e Tecnológica, Portugal
Fundação para a Ciência e a Tecnologia
Concluído
2010/01 - 2012/12 Breaking Down The Wall - Microbial Hemicellulases for saccharification
Investigador responsável
Fundação para a Ciência e a Tecnologia, I.P.
Concluído
2009/06 - 2012/12 Structural and functional study of the proteins mediating electron transfer between microorganisms and solid substrates with relevance for bio-energy production
MIT-Pt/BS-BB/0014/2008
Investigador responsável
Fundação para a Ciência e a Tecnologia, I.P.
Concluído
2009/01/01 - 2012/06/30 Marcação específica de proteínas in vitro, in vivo e à superfície das células por um novo tipo de transglutaminase isolada do esporo de Bacillus subtilis
PTDC/BIO/73946/2006
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica António Xavier, Portugal
Fundação para a Ciência e a Tecnologia
Concluído
2010/01 - 2012 Study of pH-dependent protein misfolding using state-of-the-art molecular modeling methods
Investigador
Fundação para a Ciência e a Tecnologia, I.P.
Concluído
2010/01 - 2012 Including protonation effects in the simulation of peptides and proteins in membrane environments
Investigador
Fundação para a Ciência e a Tecnologia, I.P.
Concluído
2009 - 2012 Site-specific labeling of proteins in vitro, in vivo and at the cell surface by a novel type of transglutaminase isolated from spores of Bacillus subtilis
Investigador responsável
Fundação para a Ciência e a Tecnologia, I.P.
Concluído
2009/01 - 2011/12 Investigation of redox-state-specific protein-protein interactions and energy transduction in the electron transfer chains of sulfate reducing bacteria
Investigador responsável
Fundação para a Ciência e a Tecnologia, I.P.
Concluído
2008 - 2010 Microbial enzymes involved in superoxide and nitric oxide reduction
Investigador responsável
Fundação para a Ciência e a Tecnologia, I.P.
Concluído
2007 - 2010 Towards biohydrogen production - study of a high-activity, oxygen-resistant bacterial hydrogenase
Investigador responsável
Fundação para a Ciência e a Tecnologia, I.P.
Concluído
2006 - 2010 White biotechnology for added value products from renewable plant polymers: Design of tailor-made biocatalysts and new industrial bioprocesses
FP6-2004-NMP-NI-4/02456 IP project
Investigador responsável
Concluído
2007/01 - 2008/11 Heme-copper oxygen reductases - mechanisms of electron/proton transfer and oxygen reduction Fundação para a Ciência e a Tecnologia, I.P.
2005 - 2008 Rationalization of cutinase enantioselectivity in nonaqueous media
Investigador responsável
Fundação para a Ciência e a Tecnologia, I.P.
Concluído
2005 - 2008 Nano-Engineering of Bacterial Laccases
Investigador responsável
Fundação para a Ciência e a Tecnologia, I.P.
Concluído
2005/06/01 - 2007/12/31 Racionalização da enantioselectividade da cutinase em meios não aquosos
POCI/BIO/57193/2004
Universidade Católica Portuguesa Portuguesa Centro de Biotecnologia e Química Fina, Portugal

Universidade de Lisboa Instituto Superior Técnico, Portugal

Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica António Xavier, Portugal
Fundação para a Ciência e a Tecnologia
Concluído
2003 - 2006 Increasing realism in protein modelling: including pH and redox effects into molecular dynamics simulations
Investigador
Universidade do Algarve Faculdade de Ciências e Tecnologia
Concluído
2002 - 2005 Folding, Processing and Function of Normal and Mutant Cystic Fibrosis Transmembranar Conductance Regulator: Structural Implications
Investigador responsável
Universidade do Algarve Faculdade de Ciências e Tecnologia
Concluído
2001/07 - 2004/06 Molecular modelling of key redox proteins in bacterial metabolism: methodology and applications
Provided by PTCRIS: 32789
Investigador responsável
Fundação para a Ciência e a Tecnologia, I.P.
Concluído
2001/01/01 - 2004 Electron transfer mechanisms and dynamics of a proton thruster: cytochrome c3
Investigador responsável
Universidade do Algarve Faculdade de Ciências e Tecnologia
Concluído
2001 - 2003 Novel respiratory complexes: Molecular basis for energy transduction
POCTI/BME/32789/99
Investigador responsável
Universidade do Algarve Faculdade de Ciências e Tecnologia
Concluído
2000/10/01 - 2002 Structure-function relationships of serine hydrolases in non-conventional media
Investigador responsável
Universidade do Algarve Faculdade de Ciências e Tecnologia
1996/01 - 1998/12 Molecular modelling of proteins involved in electron transfer processes
PRAXIS XXI/JNICT (PBICT/BIO/2037/95)
Investigador responsável
Concluído
1997 - 1998 Structural determinants of electron transfer interactions between [Ni-Fe] hydrogenase and cytochrome c3 from D.desulfuricans ATCC 27774
PRAXIS XXI project
Investigador responsável
Concluído
1997 - 1998 Structural determination of proteins using X-ray crystallography and its structural implications
PRAXIS XXI project
Investigador responsável
Concluído
1996 - 1998 Construction of novel redox proteins from modular building blocks
EC BIOTECNOLOGY PROGRAM AREA 6.1 project (BIO4-CT96-0413)
Investigador responsável
Concluído
1996 - 1997 Crystal structure determination and molecular modelling of proteases and electron transfer proteins
JNICT Luso-Hungariun project
Investigador responsável
Concluído
Produções

Publicações

Artigo em revista
  1. Mariana Valério; Carolina C. Buga; Manuel N. Melo; Cláudio M. Soares; Diana Lousa. "Viral entry mechanisms: the role of molecular simulation in unlocking a key step in viral infections". FEBS Open Bio (2025): https://doi.org/10.1002/2211-5463.13908.
    10.1002/2211-5463.13908
  2. Sofia Ferreira; Alexandra Balola; Anastasia Sveshnikova; Vassily Hatzimanikatis; Paulo Vilaça; Paulo Maia; Rafael Carreira; et al. "Computer-aided design and implementation of efficient biosynthetic pathways to produce high added-value products derived from tyrosine in Escherichia coli". Frontiers in Bioengineering and Biotechnology 12 (2024): https://novaresearch.unl.pt/en/publications/599ab3bf-f49c-40a9-b306-456b4e620fb9.
    10.3389/fbioe.2024.1360740
  3. Erik K.R. Hanko; João Correia; Caio S. Souza; Alison Green; Jakub Chromy; Ruth Stoney; Cunyu Yan; et al. "Microbial production of the plant flavanone hesperetin from caffeic acid". BMC Research Notes 16 1 (2023): https://novaresearch.unl.pt/en/publications/b777f9c3-87c7-4e89-96f1-e9289898384d.
    10.1186/s13104-023-06620-8
  4. Mónica Galocha; Romeu Viana; Pedro Pais; Ana Silva-Dias; Mafalda Cavalheiro; Isabel M. Miranda; Mieke Van Ende; et al. "Genomic evolution towards azole resistance in Candida glabrata clinical isolates unveils the importance of CgHxt4/6/7 in azole accumulation". Communications Biology 5 1 (2022): https://novaresearch.unl.pt/en/publications/75546f74-71bc-4c98-91e9-b842eba7f77d.
    10.1038/s42003-022-04087-0
  5. Marta C. Marques; Diana Lousa; Patrícia M. Silva; André F. Faustino; Claudio M. Soares; Nuno C. Santos. "The Importance of Lipid Conjugation on Anti-Fusion Peptides against Nipah Virus". Biomedicines (2022): https://www.mdpi.com/2227-9059/10/3/703.
    10.3390/biomedicines10030703
  6. Margarida Saramago; Vanessa G. Costa; Caio S. Souza; Cátia Bárria; Susana Domingues; Sandra C. Viegas; Diana Lousa; et al. "The nsp15 Nuclease as a Good Target to Combat SARS-CoV-2: Mechanism of Action and Its Inactivation with FDA-Approved Drugs". Microorganisms 10 2 (2022): 342-342. https://doi.org/10.3390/microorganisms10020342.
    10.3390/microorganisms10020342
  7. Mariana Valério; Luís Borges-Araújo; Manuel Nuno Melo; Diana Lousa; Claudio M. Soares. "SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessibility". Frontiers in Medical Technology 4 (2022): https://novaresearch.unl.pt/en/publications/d2226040-7e39-412b-adaf-938ab05c6f0e.
    10.3389/fmedt.2022.1009451
  8. Bárbara Abreu; Carlos Cruz; A. Sofia F. Oliveira; Claudio M. Soares. "ATP hydrolysis and nucleotide exit enhance maltose translocation in the MalFGK2E importer". Scientific Reports 11 1 (2021): https://novaresearch.unl.pt/en/publications/e34e4b21-ef3b-4ea5-93de-b7cdef1b30db.
    10.1038/s41598-021-89556-y
  9. Diana Lousa; Cláudio M. Soares. "Molecular mechanisms of the influenza fusion peptide: insights from experimental and simulation studies". FEBS Open Bio (2021): https://doi.org/10.1002/2211-5463.13323.
    10.1002/2211-5463.13323
  10. Margarida Saramago; Cátia Bárria; Vanessa G. Costa; Caio S. Souza; Sandra C. Viegas; Susana Domingues; Diana Lousa; et al. "New targets for drug design: importance of nsp14/nsp10 complex formation for the 3’-5’ exoribonucleolytic activity on SARS-CoV-2". The FEBS Journal 288 17 (2021): 5130-5147. https://doi.org/10.1111/febs.15815.
    10.1111/febs.15815
  11. Maria C. Martins; Susana F. Fernandes; Bruno A. Salgueiro; Jéssica C. Soares; Celia V. Romão; Claudio M. Soares; Diana Lousa; Filipe Folgosa; Miguel Teixeira. "The amino acids motif-32GSSYN36-in the catalytic domain of E. coli flavorubredoxin NO reductase is essential for its activity". Catalysts 11 8 (2021): https://novaresearch.unl.pt/en/publications/572948c6-9e64-4c20-aa88-2df71f28e03d.
    10.3390/catal11080926
  12. Marta Alenquer; Filipe Ferreira; Diana Lousa; Mariana Valério; Mónica Medina-Lopes; Marie Louise Bergman; Juliana Gonçalves; et al. "Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies". PLoS Pathogens 17 8 (2021): https://novaresearch.unl.pt/en/publications/376a4812-9d44-4e13-97f3-599eaba22546.
    10.1371/journal.ppat.1009772
  13. Soares, Claudio M.. "New targets for drug design: Importance of nsp14/nsp10 complex 1 formation for the 3’-5’ exoribonucleolytic activity on SARS-CoV-2". FEBS J (2021):
    Aceite para publicação
  14. Lousa, Diana; Pinto, Antónia R. T.; Campos, Sara R. R.; Baptista, António M.; Veiga, Ana S.; Castanho, Miguel A. R. B.; Soares, Cláudio M.. "Effect of pH on the influenza fusion peptide properties unveiled by constant-pH molecular dynamics simulations combined with experiment". Scientific Reports 10 1 (2020): http://dx.doi.org/10.1038/s41598-020-77040-y.
    10.1038/s41598-020-77040-y
  15. da Silva, José Adriano; Meneghetti, Mario Roberto; Soares, Cláudio Manuel. "Molecular Dynamics Simulations Suggest a Possible Role for NO in the Polyol Synthesis of Silver Nanostructures". The Journal of Physical Chemistry C 124 44 (2020): 24279-24288. http://dx.doi.org/10.1021/acs.jpcc.0c08338.
    10.1021/acs.jpcc.0c08338
  16. Barbosa, Tiago M.; Baltazar, Carla S. A.; Cruz, Davide R.; Lousa, Diana; Soares, Cláudio M.. "Studying O2 pathways in [NiFe]- and [NiFeSe]-hydrogenases". Scientific Reports 10 1 (2020): http://dx.doi.org/10.1038/s41598-020-67494-5.
    10.1038/s41598-020-67494-5
  17. Christine Orengo; Sameer Velankar; Shoshana Wodak; Vincent Zoete; Alexandre M.J.J. Bonvin; Arne Elofsson; K. Anton Feenstra; et al. "A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community)". F1000Research 9 (2020): https://novaresearch.unl.pt/en/publications/22498ed9-0a21-4959-ac41-56d86db60819.
    10.12688/f1000research.20559.1
  18. Abreu, Bárbara; Lopes, Emanuel F.; Oliveira, A. S. F.; Soares, Cláudio M.. "F508del disturbs the dynamics of the nucleotide binding domains of CFTR before and after ATP hydrolysis". Proteins: Structure, Function, and Bioinformatics 88 1 (2019): 113-126. http://dx.doi.org/10.1002/prot.25776.
    10.1002/prot.25776
  19. Pereira, F.C.; Nunes, F.; Cruz, F.; Fernandes, C.; Isidro, A.L.; Lousa, D.; Soares, C.M.; et al. "A LysM Domain intervenes in sequential protein-protein and protein-peptidoglycan interactions important for spore coat assembly in bacillus subtilis". Journal of Bacteriology 201 4 (2019): http://www.scopus.com/inward/record.url?eid=2-s2.0-85061486186&partnerID=MN8TOARS.
    10.1128/JB.00642-18
  20. Hélia F. Jeremias; L. Michel Espinoza-Fonseca; Diana Lousa; Axel Hollmann; Ana C. Coelho; Carla S. Baltazar; João D. Seixas; et al. "Study of the interactions of bovine serum albumin with a molybdenum(II) carbonyl complex by spectroscopic and molecular simulation methods". PLOS ONE 13 9 (2018): e0204624-e0204624. https://doi.org/10.1371/journal.pone.0204624.
    10.1371/journal.pone.0204624
  21. Almadanim, M.C.; Gonçalves, N.M.; Rosa, M.T.G.; Alexandre, B.M.; Cordeiro, A.M.; Rodrigues, M.; Saibo, N.J.M.; et al. "The rice cold-responsive calcium-dependent protein kinase OsCPK17 is regulated by alternative splicing and post-translational modifications". Biochimica et Biophysica Acta - Molecular Cell Research 1865 2 (2018): 231-246. http://www.scopus.com/inward/record.url?eid=2-s2.0-85034061926&partnerID=MN8TOARS.
    10.1016/j.bbamcr.2017.10.010
  22. Duarte, A.G.; Catarino, T.; White, G.F.; Lousa, D.; Neukirchen, S.; Soares, C.M.; Sousa, F.L.; Clarke, T.A.; Pereira, I.A.C.. "An electrogenic redox loop in sulfate reduction reveals a likely widespread mechanism of energy conservation". Nature Communications 9 1 (2018): http://www.scopus.com/inward/record.url?eid=2-s2.0-85058913300&partnerID=MN8TOARS.
    10.1038/s41467-018-07839-x
  23. Velada, I.; Grzebelus, D.; Lousa, D.; Soares, C.M.; Macedo, E.S.; Peixe, A.; Arnholdt-Schmitt, B.; Cardoso, H.G.. "AOX1-subfamily gene members in olea europaea cv. “Galega vulgar”—gene characterization and expression of transcripts during IBA-induced in vitro adventitious rooting". International Journal of Molecular Sciences 19 2 (2018): http://www.scopus.com/inward/record.url?eid=2-s2.0-85042233401&partnerID=MN8TOARS.
    10.3390/ijms19020597
  24. Kaur, H.; Abreu, B.; Akhmetzyanov, D.; Lakatos-Karoly, A.; Soares, C.M.; Prisner, T.; Glaubitz, C.. "Unexplored Nucleotide Binding Modes for the ABC Exporter MsbA". Journal of the American Chemical Society (2018): http://www.scopus.com/inward/record.url?eid=2-s2.0-85055666928&partnerID=MN8TOARS.
    10.1021/jacs.8b06739
  25. Sena, F.V.; Sousa, F.M.; Oliveira, A.S.F.; Soares, C.M.; Catarino, T.; Pereira, M.M.. "Regulation of the mechanism of Type-II NADH: Quinone oxidoreductase from S. aureus". Redox Biology 16 (2018): 209-214. http://www.scopus.com/inward/record.url?eid=2-s2.0-85042943505&partnerID=MN8TOARS.
    10.1016/j.redox.2018.02.004
  26. Magalhães, P.R.; Oliveira, A.S.F.; Campos, S.R.R.; Soares, C.M.; Baptista, A.M.. "Effect of a pH Gradient on the Protonation States of Cytochrome c Oxidase: A Continuum Electrostatics Study". Journal of Chemical Information and Modeling 57 2 (2017): 256-266. http://www.scopus.com/inward/record.url?eid=2-s2.0-85014290827&partnerID=MN8TOARS.
    10.1021/acs.jcim.6b00575
  27. Pereira, L.; Saraiva, I.H.; Oliveira, A.S.F.; Soares, C.M.; Louro, R.O.; Frazão, C.. "Molecular structure of FoxE, the putative iron oxidase of Rhodobacter ferrooxidans SW2". Biochimica et Biophysica Acta - Bioenergetics 1858 10 (2017): 847-853. http://www.scopus.com/inward/record.url?eid=2-s2.0-85027514977&partnerID=MN8TOARS.
    10.1016/j.bbabio.2017.07.002
  28. Marreiros, B.C.; Sena, F.V.; Sousa, F.M.; Oliveira, A.S.F.; Soares, C.M.; Batista, A.P.; Pereira, M.M.. "Structural and Functional insights into the catalytic mechanism of the Type II NADH:quinone oxidoreductase family". Scientific Reports 7 (2017): http://www.scopus.com/inward/record.url?eid=2-s2.0-85012092916&partnerID=MN8TOARS.
    10.1038/srep42303
  29. Sousa, F.M.; Sena, F.V.; Batista, A.P.; Athayde, D.; Brito, J.A.; Archer, M.; Oliveira, A.S.F.; et al. "The key role of glutamate 172 in the mechanism of type II NADH:quinone oxidoreductase of Staphylococcus aureus". Biochimica et Biophysica Acta - Bioenergetics 1858 10 (2017): 823-832. http://www.scopus.com/inward/record.url?eid=2-s2.0-85027494279&partnerID=MN8TOARS.
    10.1016/j.bbabio.2017.08.002
  30. Lousa, D.; Pinto, A.R.T.; Victor, B.L.; Laio, A.; Veiga, A.S.; Castanho, M.A.R.B.; Soares, C.M.. "Fusing simulation and experiment: The effect of mutations on the structure and activity of the influenza fusion peptide". Scientific Reports 6 (2016): http://www.scopus.com/inward/record.url?eid=2-s2.0-84975041212&partnerID=MN8TOARS.
    10.1038/srep28099
  31. Oliveira, A.S.F.; Campos, S.R.R.; Baptista, A.M.; Soares, C.M.. "Coupling between protonation and conformation in cytochrome c oxidase: Insights from constant-pH MD simulations". Biochimica et Biophysica Acta - Bioenergetics 1857 6 (2016): 759-771. http://www.scopus.com/inward/record.url?eid=2-s2.0-84964689558&partnerID=MN8TOARS.
    10.1016/j.bbabio.2016.03.024
  32. Romão, C.V.; Vicente, J.B.; Borges, P.T.; Victor, B.L.; Lamosa, P.; Silva, E.; Pereira, L.; et al. "Structure of Escherichia coli Flavodiiron Nitric Oxide Reductase". Journal of Molecular Biology 428 23 (2016): 4686-4707. http://www.scopus.com/inward/record.url?eid=2-s2.0-84996538192&partnerID=MN8TOARS.
    10.1016/j.jmb.2016.10.008
  33. Fernandes, C.G.; Plácido, D.; Lousa, D.; Brito, J.A.; Isidro, A.; Soares, C.M.; Pohl, J.; et al. "Structural and Functional Characterization of an Ancient Bacterial Transglutaminase Sheds Light on the Minimal Requirements for Protein Cross-Linking". Biochemistry 54 37 (2015): 5723-5734. http://www.scopus.com/inward/record.url?eid=2-s2.0-84942100927&partnerID=MN8TOARS.
    10.1021/acs.biochem.5b00661
  34. Victor, B.L.; Lousa, D.; Antunes, J.M.; Soares, C.M.. "Self-assembly molecular dynamics simulations shed light into the interaction of the influenza fusion peptide with a membrane bilayer". Journal of Chemical Information and Modeling 55 4 (2015): 795-805. http://www.scopus.com/inward/record.url?eid=2-s2.0-84928686003&partnerID=MN8TOARS.
    10.1021/ci500756v
  35. Alves, M.N.; Neto, S.E.; Alves, A.S.; Fonseca, B.M.; Carrêlo, A.; Pacheco, I.; Paquete, C.M.; Soares, C.M.; Louro, R.O.. "Characterization of the periplasmic redox network that sustains the versatile anaerobic metabolism of Shewanella oneidensis MR-1". Frontiers in Microbiology 6 JUN (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84937144196&partnerID=MN8TOARS.
    10.3389/fmicb.2015.00665
  36. Nobre, L.S.; Lousa, D.; Pacheco, I.; Soares, C.M.; Teixeira, M.; Saraiva, L.M.. "Insights into the structure of the diiron site of RIC from Escherichia coli". FEBS Letters 589 4 (2015): 426-431. http://www.scopus.com/inward/record.url?eid=2-s2.0-84964273503&partnerID=MN8TOARS.
    10.1016/j.febslet.2014.12.028
  37. Oliveira, A.S.F.; Damas, J.M.; Baptista, A.M.; Soares, C.M.. "Exploring O 2 Diffusion in A-Type Cytochrome c Oxidases: Molecular Dynamics Simulations Uncover Two Alternative Channels towards the Binuclear Site". PLoS Computational Biology 10 12 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84919667074&partnerID=MN8TOARS.
    10.1371/journal.pcbi.1004010
  38. Damas, J.M.; Baptista, A.M.; Soares, C.M.. "The pathway for O2 diffusion inside CotA laccase and possible implications on the multicopper oxidases family". Journal of Chemical Theory and Computation 10 8 (2014): 3525-3531. http://www.scopus.com/inward/record.url?eid=2-s2.0-84906245108&partnerID=MN8TOARS.
    10.1021/ct500196e
  39. McVey, C.E.; Ferreira, M.J.; Correia, B.; Lahiri, S.; De Sanctis, D.; Carrondo, M.A.; Lindley, P.F.; et al. "The importance of the Abn2 calcium cluster in the endo-1,5-arabinanase activity from Bacillus subtilis Topical Issue in honor of Ivano Bertini. Guest editors: Lucia Banci, Claudio Luchinat". Journal of Biological Inorganic Chemistry 19 4-5 (2014): 505-513. http://www.scopus.com/inward/record.url?eid=2-s2.0-84901949682&partnerID=MN8TOARS.
    10.1007/s00775-014-1105-x
  40. Paquete, C.M.; Fonseca, B.M.; Cruz, D.R.; Pereira, T.M.; Pacheco, I.; Soares, C.M.; Louro, R.O.. "Exploring the molecular mechanisms of electron shuttling across the microbe/metal space". Frontiers in Microbiology 5 JUN (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84904907260&partnerID=MN8TOARS.
    10.3389/fmicb.2014.00318
  41. Damas, J.M.; Filipe, L.C.S.; Campos, S.R.R.; Lousa, D.; Victor, B.L.; Baptista, A.M.; Soares, C.M.. "Predicting the thermodynamics and kinetics of helix formation in a cyclic peptide model". Journal of Chemical Theory and Computation 9 11 (2013): 5148-5157. http://www.scopus.com/inward/record.url?eid=2-s2.0-84887835236&partnerID=MN8TOARS.
    10.1021/ct400529k
  42. Lousa, D.; Baptista, A.M.; Soares, C.M.. "A molecular perspective on nonaqueous biocatalysis: Contributions from simulation studies". Physical Chemistry Chemical Physics 15 33 (2013): 13723-13736. http://www.scopus.com/inward/record.url?eid=2-s2.0-84881248110&partnerID=MN8TOARS.
    10.1039/c3cp51761f
  43. Volkers, G.; Damas, J.M.; Palm, G.J.; Panjikar, S.; Soares, C.M.; Hinrichs, W.. "Putative dioxygen-binding sites and recognition of tigecycline and minocycline in the tetracycline-degrading monooxygenase TetX". Acta Crystallographica Section D: Biological Crystallography 69 9 (2013): 1758-1767. http://www.scopus.com/inward/record.url?eid=2-s2.0-84883589322&partnerID=MN8TOARS.
    10.1107/S0907444913013802
  44. Fonseca, B.M.; Paquete, C.M.; Neto, S.E.; Pacheco, I.; Soares, C.M.; Louro, R.O.. "Mind the gap: Cytochrome interactions reveal electron pathways across the periplasm of Shewanella oneidensis MR-1". Biochemical Journal 449 1 (2013): 101-108. http://www.scopus.com/inward/record.url?eid=2-s2.0-84870912011&partnerID=MN8TOARS.
    10.1042/BJ20121467
  45. Gutiérrez-Sanz, O.; Marques, M.C.; Baltazar, C.S.A.; Fernández, V.M.; Soares, C.M.; Pereira, I.A.C.; De Lacey, A.L.. "Influence of the protein structure surrounding the active site on the catalytic activity of [NiFeSe] hydrogenases". Journal of Biological Inorganic Chemistry 18 4 (2013): 419-427. http://www.scopus.com/inward/record.url?eid=2-s2.0-84876496433&partnerID=MN8TOARS.
    10.1007/s00775-013-0986-4
  46. Azoia, N.G.; Fernandes, M.M.; Micaêlo, N.M.; Soares, C.M.; Cavaco-Paulo, A.. "Molecular modeling of hair keratin/peptide complex: Using MM-PBSA calculations to describe experimental binding results". Proteins: Structure, Function and Bioinformatics 80 5 (2012): 1409-1417. http://www.scopus.com/inward/record.url?eid=2-s2.0-84859442401&partnerID=MN8TOARS.
    10.1002/prot.24037
  47. Pires, S.; Habjanic, J.; Sezer, M.; Soares, C.M.; Hemmingsen, L.; Iranzo, O.. "Design of a peptidic turn with high affinity for HgII". Inorganic Chemistry 51 21 (2012): 11339-11348. http://www.scopus.com/inward/record.url?eid=2-s2.0-84868354575&partnerID=MN8TOARS.
    10.1021/ic3008014
  48. Lousa, D.; Cianci, M.; Helliwell, J.R.; Halling, P.J.; Baptista, A.M.; Soares, C.M.. "Interaction of counterions with subtilisin in acetonitrile: Insights from molecular dynamics simulations". Journal of Physical Chemistry B 116 20 (2012): 5838-5848. http://www.scopus.com/inward/record.url?eid=2-s2.0-84862279541&partnerID=MN8TOARS.
    10.1021/jp303008g
  49. Baltazar, C.S.A.; Teixeira, V.H.; Soares, C.M.. "Structural features of [NiFeSe] and [NiFe] hydrogenases determining their different properties: A computational approach". Journal of Biological Inorganic Chemistry 17 4 (2012): 543-555. http://www.scopus.com/inward/record.url?eid=2-s2.0-84862511693&partnerID=MN8TOARS.
    10.1007/s00775-012-0875-2
  50. Lousa, D.; Baptista, A.M.; Soares, C.M.. "Analyzing the molecular basis of enzyme stability in ethanol/water mixtures using molecular dynamics simulations". Journal of Chemical Information and Modeling 52 2 (2012): 465-473. http://www.scopus.com/inward/record.url?eid=2-s2.0-84857583770&partnerID=MN8TOARS.
    10.1021/ci200455z
  51. Soares, C.M.; Baptista, A.M.. "Simulation of multihaem cytochromes". FEBS Letters 586 5 (2012): 510-518. http://www.scopus.com/inward/record.url?eid=2-s2.0-84857916893&partnerID=MN8TOARS.
    10.1016/j.febslet.2011.10.019
  52. Silva, C.S.; Damas, J.M.; Chen, Z.; Brissos, V.; Martins, L.O.; Soares, C.M.; Lindley, P.F.; Bento, I.. "The role of Asp116 in the reductive cleavage of dioxygen to water in CotA laccase: Assistance during the proton-transfer mechanism". Acta Crystallographica Section D: Biological Crystallography 68 2 (2012): 186-193. http://www.scopus.com/inward/record.url?eid=2-s2.0-84863011701&partnerID=MN8TOARS.
    10.1107/S0907444911054503
  53. Campos, E.; Asandei, A.; McVey, C.E.; Dias, J.C.; Oliveira, A.S.F.; Soares, C.M.; Luchian, T.; Astier, Y.. "The role of lys147 in the interaction between MPSA-gold nanoparticles and the a-hemolysin nanopore". Langmuir 28 44 (2012): 15643-15650. http://www.scopus.com/inward/record.url?eid=2-s2.0-84868607116&partnerID=MN8TOARS.
    10.1021/la302613g
  54. Victor, B.L.; Baptista, A.M.; Soares, C.M.. "Structural determinants for the membrane insertion of the transmembrane peptide of hemagglutinin from influenza virus". Journal of Chemical Information and Modeling 52 11 (2012): 3001-3012. http://www.scopus.com/inward/record.url?eid=2-s2.0-84870015416&partnerID=MN8TOARS.
    10.1021/ci3003396
  55. Damas, J.M.; Oliveira, A.S.F.; Baptista, A.M.; Soares, C.M.. "Structural consequences of ATP hydrolysis on the ABC transporter NBD dimer: Molecular dynamics studies of HlyB". Protein Science 20 7 (2011): 1220-1230. http://www.scopus.com/inward/record.url?eid=2-s2.0-79959352522&partnerID=MN8TOARS.
    10.1002/pro.650
  56. Oliveira, A.S.F.; Baptista, A.M.; Soares, C.M.. "Inter-domain communication mechanisms in an ABC importer: A molecular dynamics study of the MalFGK 2E complex". PLoS Computational Biology 7 8 (2011): http://www.scopus.com/inward/record.url?eid=2-s2.0-80052311546&partnerID=MN8TOARS.
    10.1371/journal.pcbi.1002128
  57. Baltazar, C.S.A.; Marques, M.C.; Soares, C.M.; DeLacey, A.M.; Pereira, I.A.C.; Matias, P.M.. "Nickel-iron-selenium hydrogenases - An overview". European Journal of Inorganic Chemistry 7 (2011): 948-962. http://www.scopus.com/inward/record.url?eid=2-s2.0-79951883377&partnerID=MN8TOARS.
    10.1002/ejic.201001127
  58. Oliveira, A.S.; Baptista, A.M.; Soares, C.M.. "Conformational changes induced by ATP-hydrolysis in an ABC transporter: A molecular dynamics study of the Sav1866 exporter". Proteins: Structure, Function and Bioinformatics 79 6 (2011): 1977-1990. http://www.scopus.com/inward/record.url?eid=2-s2.0-79955741987&partnerID=MN8TOARS.
    10.1002/prot.23023
  59. Lousa, D.; Baptista, A.M.; Soares, C.M.. "Structural determinants of ligand imprinting: A molecular dynamics simulation study of subtilisin in aqueous and apolar solvents". Protein Science 20 2 (2011): 379-386. http://www.scopus.com/inward/record.url?eid=2-s2.0-79251557782&partnerID=MN8TOARS.
    10.1002/pro.569
  60. Varanda, C.; Félix, M.R.; Soares, C.M.; Oliveira, S.; Clara, M.I.. "Specific amino acids of Olive mild mosaic virus coat protein are involved in transmission by Olpidium brassicae". Journal of General Virology 92 9 (2011): 2209-2213. http://www.scopus.com/inward/record.url?eid=2-s2.0-80051729438&partnerID=MN8TOARS.
    10.1099/vir.0.032284-0
  61. Bento, I.; Silva, C.S.; Chen, Z.; Martins, L.O.; Lindley, P.F.; Soares, C.M.. "Mechanisms underlying dioxygen reduction in laccases. Structural and modelling studies focusing on proton transfer". BMC Structural Biology 10 (2010): http://www.scopus.com/inward/record.url?eid=2-s2.0-77956488302&partnerID=MN8TOARS.
    10.1186/1472-6807-10-28
  62. Fernandes, A.T.; Damas, J.M.; Todorovic, S.; Huber, R.; Baratto, M.C.; Pogni, R.; Soares, C.M.; Martins, L.O.. "The multicopper oxidase from the archaeon Pyrobaculum aerophilum shows nitrous oxide reductase activity". FEBS Journal 277 15 (2010): 3176-3189. http://www.scopus.com/inward/record.url?eid=2-s2.0-77954726299&partnerID=MN8TOARS.
    10.1111/j.1742-4658.2010.07725.x
  63. MacHuqueiro, M.; Campos, S.R.R.; Soares, C.M.; Baptista, A.M.. "Membrane-induced conformational changes of kyotorphin revealed by molecular dynamics simulations". Journal of Physical Chemistry B 114 35 (2010): 11659-11667. http://www.scopus.com/inward/record.url?eid=2-s2.0-77956326420&partnerID=MN8TOARS.
    10.1021/jp104418g
  64. Oliveira, A.S.F.; Baptista, A.M.; Soares, C.M.. "Insights into the molecular mechanism of an ABC transporter: Conformational changes in the NBD dimer of mj0796". Journal of Physical Chemistry B 114 16 (2010): 5486-5496. http://www.scopus.com/inward/record.url?eid=2-s2.0-77951539821&partnerID=MN8TOARS.
    10.1021/jp905735y
  65. Gonçalves, S.; Borges, N.; Esteves, A.M.; Victor, B.L.; Soares, C.M.; Santos, H.; Matias, P.M.. "Structural analysis of Thermus thermophilus HB27 mannosyl-3- phosphoglycerate synthase provides evidence for a second catalytic metal ion and new insight into the retaining mechanism of glycosyltransferases". Journal of Biological Chemistry 285 23 (2010): 17857-17868. http://www.scopus.com/inward/record.url?eid=2-s2.0-77952938697&partnerID=MN8TOARS.
    10.1074/jbc.M109.095976
  66. Fonseca, B.M.; Saraiva, I.H.; Paquete, C.M.; Soares, C.M.; Pacheco, I.; Salgueiro, C.A.; Louro, R.O.. "The tetraheme cytochrome from Shewanella oneidensis MR-1 shows thermodynamic bias for functional specificity of the hemes". Journal of Biological Inorganic Chemistry 14 3 (2009): 375-385. http://www.scopus.com/inward/record.url?eid=2-s2.0-61849083078&partnerID=MN8TOARS.
    10.1007/s00775-008-0455-7
  67. Victor, B.L.; Baptista, A.M.; Soares, C.M.. "Dioxygen and nitric oxide pathways and affinity to the catalytic site of rubredoxin: Oxygen oxidoreductase from Desulfovibrio gigas". Journal of Biological Inorganic Chemistry 14 6 (2009): 853-862. http://www.scopus.com/inward/record.url?eid=2-s2.0-70349289240&partnerID=MN8TOARS.
    10.1007/s00775-009-0497-5
  68. Rodrigues, J.V.; Victor, B.L.; Huber, H.; Saraiva, L.M.; Soares, C.M.; Cabelli, D.E.; Teixeira, M.. "Superoxide reduction by Nanoarchaeum equitans neelaredoxin, an enzyme lacking the highly conserved glutamate iron ligand". Journal of Biological Inorganic Chemistry 13 2 (2008): 219-228. http://www.scopus.com/inward/record.url?eid=2-s2.0-38649136959&partnerID=MN8TOARS.
    10.1007/s00775-007-0313-z
  69. Teixeira, V.H.; Soares, C.M.; Baptista, A.M.. "Proton pathways in a [NiFe]-hydrogenase: A theoretical study". Proteins: Structure, Function and Genetics 70 3 (2008): 1010-1022. http://www.scopus.com/inward/record.url?eid=2-s2.0-38549139111&partnerID=MN8TOARS.
    10.1002/prot.21588
  70. Durão, P.; Chen, Z.; Silva, C.S.; Soares, C.M.; Pereira, M.M.; Todorovic, S.; Hildebrandt, P.; et al. "Proximal mutations at the type 1 copper site of CotA laccase: Spectroscopic, redox, kinetic and structural characterization of I494A and L386A mutants". Biochemical Journal 412 2 (2008): 339-346. http://www.scopus.com/inward/record.url?eid=2-s2.0-44449110619&partnerID=MN8TOARS.
    10.1042/BJ20080166
  71. Micaelo, N.M.; Victor, B.L.; Soares, C.M.. "Protein thermal stabilization by charged compatible solutes: Computational studies in rubredoxin from Desulfovibrio gigas". Proteins: Structure, Function and Genetics 72 2 (2008): 580-588. http://www.scopus.com/inward/record.url?eid=2-s2.0-46449090359&partnerID=MN8TOARS.
    10.1002/prot.21948
  72. Micaêlo, N.M.; Soares, C.M.. "Protein structure and dynamics in ionic liquids. Insights from molecular dynamics simulation studies". Journal of Physical Chemistry B 112 9 (2008): 2566-2572. http://www.scopus.com/inward/record.url?eid=2-s2.0-41549135319&partnerID=MN8TOARS.
    10.1021/jp0766050
  73. Escrevente, C.; Morais, V.A.; Keller, S.; Soares, C.M.; Altevogt, P.; Costa, J.. "Functional role of N-glycosylation from ADAM10 in processing, localization and activity of the enzyme". Biochimica et Biophysica Acta - General Subjects 1780 6 (2008): 905-913. http://www.scopus.com/inward/record.url?eid=2-s2.0-43149108354&partnerID=MN8TOARS.
    10.1016/j.bbagen.2008.03.004
  74. Broco, M.; Soares, C.M.; Oliveira, S.; Mayhew, S.G.; Rodrigues-Pousada, C.. "Molecular determinants for FMN-binding in Desulfovibrio gigas flavoredoxin". FEBS Letters 581 23 (2007): 4397-4402. http://www.scopus.com/inward/record.url?eid=2-s2.0-34548384271&partnerID=MN8TOARS.
    10.1016/j.febslet.2007.08.009
  75. Gaspar, P.; Neves, A.R.; Shearman, C.A.; Gasson, M.J.; Baptista, A.M.; Turner, D.L.; Soares, C.M.; Santos, H.. "The lactate dehydrogenases encoded by the ldh and ldhB genes in Lactococcus lactis exhibit distinct regulation and catalytic properties - Comparative modeling to probe the molecular basis". FEBS Journal 274 22 (2007): 5924-5936. http://www.scopus.com/inward/record.url?eid=2-s2.0-35748951589&partnerID=MN8TOARS.
    10.1111/j.1742-4658.2007.06115.x
  76. Fernandes, A.T.; Soares, C.M.; Pereira, M.M.; Huber, R.; Grass, G.; Martins, L.O.. "A robust metallo-oxidase from the hyperthermophilic bacterium Aquifex aeolicus". FEBS Journal 274 11 (2007): 2683-2694. http://www.scopus.com/inward/record.url?eid=2-s2.0-34249108880&partnerID=MN8TOARS.
    10.1111/j.1742-4658.2007.05803.x
  77. Franco, I.S.; Mota, L.J.; Soares, C.M.; de Sá-Nogueira, I.. "Probing key DNA contacts in AraR-mediated transcriptional repression of the Bacillus subtilis arabinose regulon". Nucleic Acids Research 35 14 (2007): 4755-4766. http://www.scopus.com/inward/record.url?eid=2-s2.0-34547863494&partnerID=MN8TOARS.
    10.1093/nar/gkm509
  78. Araújo, R.; Silva, C.; O'Neill, A.; Micaelo, N.; Guebitz, G.; Soares, C.M.; Casal, M.; Cavaco-Paulo, A.. "Tailoring cutinase activity towards polyethylene terephthalate and polyamide 6,6 fibers". Journal of Biotechnology 128 4 (2007): 849-857. http://www.scopus.com/inward/record.url?eid=2-s2.0-33847353686&partnerID=MN8TOARS.
    10.1016/j.jbiotec.2006.12.028
  79. Micaêlo, N.M.; Soares, C.M.. "Modeling hydration mechanisms of enzymes in nonpolar and polar organic solvents". FEBS Journal 274 9 (2007): 2424-2436. http://www.scopus.com/inward/record.url?eid=2-s2.0-34247363159&partnerID=MN8TOARS.
    10.1111/j.1742-4658.2007.05781.x
  80. Teixeira, V.H.; Baptista, A.M.; Soares, C.M.. "Pathways of H2 toward the active site of [NiFe]-hydrogenase". Biophysical Journal 91 6 (2006): 2035-2045. http://www.scopus.com/inward/record.url?eid=2-s2.0-33748456960&partnerID=MN8TOARS.
    10.1529/biophysj.106.084376
  81. Roxo-Rosa, M.; Xu, Z.; Schmidt, A.; Neto, M.; Cai, Z.; Soares, C.M.; Sheppard, D.H.; Amaral, M.D.. "Revertant mutants G550E and 4RK rescue cystic fibrosis mutants in the first nucleotide-binding domain of CFTR by different mechanisms". Proceedings of the National Academy of Sciences of the United States of America 103 47 (2006): 17891-17896. http://www.scopus.com/inward/record.url?eid=2-s2.0-33845197320&partnerID=MN8TOARS.
    10.1073/pnas.0608312103
  82. Micaelo, N.M.; Baptists, A.M.; Soares, C.M.. "Parametrization of 1-butyl-3-methylimidazolium hexafluorophosphate/nitrate ionic liquid for the GROMOS force field". Journal of Physical Chemistry B 110 29 (2006): 14444-14451. http://www.scopus.com/inward/record.url?eid=2-s2.0-33746915678&partnerID=MN8TOARS.
    10.1021/jp061869s
  83. Rocha, R.; Leal, S.S.; Teixeira, V.H.; Regalla, M.; Huber, H.; Baptista, A.M.; Soares, C.M.; Gomes, C.M.. "Natural domain design: Enhanced thermal stability of a zinc-lacking ferredoxin isoform shows that a hydrophobic core efficiently replaces the structural metal site". Biochemistry 45 34 (2006): 10376-10384. http://www.scopus.com/inward/record.url?eid=2-s2.0-33748694511&partnerID=MN8TOARS.
    10.1021/bi0610698
  84. Franco, I.S.; Mota, L.J.; Soares, C.M.; De Sá-Nogueira, I.. "Functional domains of the Bacillus subtilis transcription factor AraR and identification of amino acids important for nucleoprotein complex assembly and effector binding". Journal of Bacteriology 188 8 (2006): 3024-3036. http://www.scopus.com/inward/record.url?eid=2-s2.0-33646003235&partnerID=MN8TOARS.
    10.1128/JB.188.8.3024-3036.2006
  85. Iley, J.; Moreira, R.; Martins, L.; Guedes, R.C.; Soares, C.M.. "The Bsmoc group as a novel scaffold for the design of irreversible inhibitors of cysteine proteases". Bioorganic and Medicinal Chemistry Letters 16 10 (2006): 2738-2741. http://www.scopus.com/inward/record.url?eid=2-s2.0-33645857658&partnerID=MN8TOARS.
    10.1016/j.bmcl.2006.02.007
  86. Lopes, S.C.D.N.; Soares, C.M.; Baptista, A.M.; Goormaghtigh, E.; Cabral, B.J.C.; Castanho, M.A.R.B.. "Conformational and orientational guidance of the analgesic dipeptide kyotorphin induced by lipidic membranes: Putative correlation toward receptor docking". Journal of Physical Chemistry B 110 7 (2006): 3385-3394. http://www.scopus.com/inward/record.url?eid=2-s2.0-33644895138&partnerID=MN8TOARS.
    10.1021/jp053651w
  87. Valente, F.M.A.; Oliveira, A.S.F.; Gnadt, N.; Pacheco, I.; Coelho, A.V.; Xavier, A.V.; Teixeira, M.; Soares, C.M.; Pereira, I.A.C.. "Hydrogenases in Desulfovibrio vulgaris Hildenborough: Structural and physiologic characterisation of the membrane-bound [NiFeSe] hydrogenase". Journal of Biological Inorganic Chemistry 10 6 (2005): 667-682. http://www.scopus.com/inward/record.url?eid=2-s2.0-27944451793&partnerID=MN8TOARS.
    10.1007/s00775-005-0022-4
  88. Matias, P.M.; Pereira, I.A.C.; Soares, C.M.; Carrondo, M.A.. "Sulphate respiration from hydrogen in Desulfovibrio bacteria: A structural biology overview". Progress in Biophysics and Molecular Biology 89 3 (2005): 292-329. http://www.scopus.com/inward/record.url?eid=2-s2.0-20444385906&partnerID=MN8TOARS.
    10.1016/j.pbiomolbio.2004.11.003
  89. Teixeira, V.H.; Cunha, C.A.; Machuqueiro, M.; Oliveira, A.S.F.; Victor, B.L.; Soares, C.M.; Baptista, A.M.. "On the use of different dielectric constants for computing individual and pairwise terms in poisson-boltzmann studies of protein ionization equilibrium". Journal of Physical Chemistry B 109 30 (2005): 14691-14706. http://www.scopus.com/inward/record.url?eid=2-s2.0-23844500381&partnerID=MN8TOARS.
    10.1021/jp052259f
  90. Kirichenko, A.V.; Pfitzner, U.; Ludwig, B.; Soares, C.M.; Vygodina, T.V.; Konstantinov, A.A.. "Cytochrome c oxidase as a calcium binding protein. Studies on the role of a conserved aspartate in helices XI-XII cytoplasmic loop in cation binding". Biochemistry 44 37 (2005): 12391-12401. http://www.scopus.com/inward/record.url?eid=2-s2.0-24944511130&partnerID=MN8TOARS.
    10.1021/bi050376v
  91. Rivas, L.; Soares, C.M.; Baptista, A.M.; Simaan, J.; Di Paolo, R.E.; Murgida, D.H.; Hildebrandt, P.. "Electric-field-induced redox potential shifts of tetraheme cytochromes c3immobilized on self-assembled monolayers: Surface-enhanced resonance raman spectroscopy and simulation studies". Biophysical Journal 88 6 (2005): 4188-4199. http://www.scopus.com/inward/record.url?eid=2-s2.0-22244481835&partnerID=MN8TOARS.
    10.1529/biophysj.104.057232
  92. Micaelo, N.M.; Teixeira, V.H.; Baptista, A.M.; Soares, C.M.. "Water dependent properties of cutinase in nonaqueous solvents: A computational study of enantioselectivity". Biophysical Journal 89 2 (2005): 999-1008. http://www.scopus.com/inward/record.url?eid=2-s2.0-23244449490&partnerID=MN8TOARS.
    10.1529/biophysj.105.063297
  93. Oliveira, A.S.F.; Teixeira, V.H.; Baptista, A.M.; Soares, C.M.. "Reorganization and conformational changes in the reduction of tetraheme cytochromes". Biophysical Journal 89 6 (2005): 3919-3930. http://www.scopus.com/inward/record.url?eid=2-s2.0-28444483273&partnerID=MN8TOARS.
    10.1529/biophysj.105.065144
  94. Victor, Bruno L.; Baptista, António M.; Soares, Cláudio M.. "Theoretical Identification of Proton Channels in the Quinol Oxidase aa3 from Acidianus ambivalens". Biophysical Journal 87 6 (2004): 4316-4325. http://dx.doi.org/10.1529/biophysj.104.049353.
    10.1529/biophysj.104.049353
  95. Serrano, M.; Neves, A.; Soares, C. M.; Moran, C. P.; Henriques, A. O.. "Role of the Anti-Sigma Factor SpoIIAB in Regulation of  G during Bacillus subtilis Sporulation". Journal of Bacteriology 186 12 (2004): 4000-4013. http://dx.doi.org/10.1128/jb.186.12.4000-4013.2004.
    10.1128/jb.186.12.4000-4013.2004
  96. Serrano, M.; Neves, A.; Soares, C.M.; Moran Jr., C.P.; Henriques, A.O.. "Role of the anti-sigma factor SpoIIAB in regulation of sG during Bacillus subtilis sporulation". Journal of Bacteriology 186 12 (2004): 4000-4013. http://www.scopus.com/inward/record.url?eid=2-s2.0-2942602687&partnerID=MN8TOARS.
    10.1128/JB.186.12.4000-4013.2004
  97. Victor, B.L.; Baptista, A.M.; Soares, C.M.. "Theoretical identification of proton channels in the quinol oxidase aa 3 from Acidianus ambivalens". Biophysical Journal 87 6 (2004): 4316-4325. http://www.scopus.com/inward/record.url?eid=2-s2.0-10044240740&partnerID=MN8TOARS.
    10.1529/biophysj.104.049353
  98. Soares, C.M.; Baptista, A.M.; Pereira, M.M.; Teixeira, M.. "Investigation of protonatable residues in Rhodothermus marinus caa 3 haem-copper oxygen reductase: Comparism with Paracoccus denitrificans aa3 haem-copper oxygen reductase". Journal of Biological Inorganic Chemistry 9 2 (2004): 124-134. http://www.scopus.com/inward/record.url?eid=2-s2.0-1542298196&partnerID=MN8TOARS.
    10.1007/s00775-003-0509-9
  99. Bento, I.; Matias, P.M.; Baptista, A.M.; Da Costa, P.N.; Van Dongen, W.M.A.M.; Saraiva, L.M.; Schneider, T.R.; Soares, C.M.; Carrondo, M.A.. "Molecular Basis for Redox-Bohr and Cooperative Effects in Cytochrome c 3 from Desulfovibrio desulfuricans ATCC 27774: Crystallographic and Modeling Studies of Oxidized and Reduced High-Resolution Structures at pH 7.6". Proteins: Structure, Function and Genetics 54 1 (2004): 135-152. http://www.scopus.com/inward/record.url?eid=2-s2.0-0348047621&partnerID=MN8TOARS.
    10.1002/prot.10431
  100. Vidinha, P.; Harper, N.; Micaelo, N.M.; Lourenco, N.M.T.; Gomes Da Silva, M.D.R.; Cabral, J.; Afonso, C.A.M.; Soares, C.M.; Barreiros, S.. "Effect of Immobilization Support, Water Activity, and Enzyme Ionization State on Cutinase Activity and Enantioselectivity in Organic Media". Biotechnology and Bioengineering 85 4 (2004): 442-449. http://www.scopus.com/inward/record.url?eid=2-s2.0-0442278161&partnerID=MN8TOARS.
    10.1002/bit.10780
  101. Teixeira, V.H.; Baptista, A.M.; Soares, C.M.. "Modeling Electron Transfer Thermodynamics in Protein Complexes: Interaction between Two Cytochromes c3". Biophysical Journal 86 5 (2004): 2773-2785. http://www.scopus.com/inward/record.url?eid=2-s2.0-2142644598&partnerID=MN8TOARS.
    10.1016/S0006-3495(04)74331-3
  102. Bento, I.; Teixeira, V.H.; Baptista, A.M.; Soares, C.M.; Matias, P.M.; Carrondo, M.A.. "Redox-Bohr and other cooperativity effects in the nine-heme cytochrome c from Desulfovibrio desulfuricans ATCC 27774: Crystallographic and modeling studies". Journal of Biological Chemistry 278 38 (2003): 36455-36469. http://www.scopus.com/inward/record.url?eid=2-s2.0-0141815636&partnerID=MN8TOARS.
    10.1074/jbc.M301745200
  103. Price, N.J.; Pinheiro, C.; Soares, C.M.; Ashford, D.A.; Ricardo, C.P.; Jackson, P.A.. "A Biochemical and Molecular Characterization of LEP1, an Extensin Peroxidase from Lupin". Journal of Biological Chemistry 278 42 (2003): 41389-41399. http://www.scopus.com/inward/record.url?eid=2-s2.0-0142103316&partnerID=MN8TOARS.
    10.1074/jbc.M304519200
  104. Victor, B.L.; Vicente, J.B.; Rodrigues, R.; Oliveira, S.; Rodrigues-Pousada, C.; Frazão, C.; Gomes, C.M.; Teixeira, M.; Soares, C.M.. "Docking and electron transfer studies between rubredoxin and rubredoxin:oxygen oxidoreductase". Journal of Biological Inorganic Chemistry 8 4 (2003): 475-488. http://www.scopus.com/inward/record.url?eid=2-s2.0-0037951339&partnerID=MN8TOARS.
  105. Soares, C.M.; Teixeira, V.H.; Baptista, A.M.. "Protein structure and dynamics in nonaqueous solvents: Insights from molecular dynamics simulation studies". Biophysical Journal 84 3 (2003): 1628-1641. http://www.scopus.com/inward/record.url?eid=2-s2.0-0037342275&partnerID=MN8TOARS.
  106. Martins, L.O.; Soares, C.M.; Pereira, M.M.; Teixeira, M.; Costa, T.; Jones, G.H.; Henriques, A.O.. "Molecular and biochemical characterization of a highly stable bacterial laccase that occurs as a structural component of the Bacillus subtilis endospore coat". Journal of Biological Chemistry 277 21 (2002): 18849-18859. http://www.scopus.com/inward/record.url?eid=2-s2.0-0037166265&partnerID=MN8TOARS.
    10.1074/jbc.M200827200
  107. Baptista, A.M.; Teixeira, V.H.; Soares, C.M.. "Constant-pH molecular dynamics using stochastic titration". Journal of Chemical Physics 117 9 (2002): 4184-4200. http://www.scopus.com/inward/record.url?eid=2-s2.0-0036732086&partnerID=MN8TOARS.
    10.1063/1.1497164
  108. Teixeira, V.H.; Soares, C.M.; Baptista, A.M.. "Studies of the reduction and protonation behavior of tetraheme cytochromes using atomic detail". Journal of Biological Inorganic Chemistry 7 1-2 (2002): 200-216. http://www.scopus.com/inward/record.url?eid=2-s2.0-0036359052&partnerID=MN8TOARS.
    10.1007/s007750100287
  109. Santana, M.; Pereira, M.M.; Elias, N.P.; Soares, C.M.; Teixeira, M.. "Gene cluster of Rhodothermus marinus high-potential iron-sulfur protein:oxygen oxidoreductase, a caa3-type oxidase belonging to the superfamily of heme-copper oxidases". Journal of Bacteriology 183 2 (2001): 687-699. http://www.scopus.com/inward/record.url?eid=2-s2.0-0035171171&partnerID=MN8TOARS.
    10.1128/JB.183.2.687-699.2001
  110. Louro, R.O.; Bento, I.; Matias, P.M.; Catarino, T.; Baptista, A.M.; Soares, C.M.; Carrondo, M.A.; Turner, D.L.; Xavier, A.V.. "Conformational Component in the Coupled Transfer of Multiple Electrons and Protons in a Monomeric Tetraheme Cytochrome". Journal of Biological Chemistry 276 47 (2001): 44044-44051. http://www.scopus.com/inward/record.url?eid=2-s2.0-0035941269&partnerID=MN8TOARS.
    10.1074/jbc.M107136200
  111. Abreu, I.A.; Saraiva, L.M.; Soares, C.M.; Teixeira, M.; Cabelli, D.E.. "The Mechanism of Superoxide Scavenging by Archaeoglobus fulgidus Neelaredoxin". Journal of Biological Chemistry 276 42 (2001): 38995-39001. http://www.scopus.com/inward/record.url?eid=2-s2.0-0035914396&partnerID=MN8TOARS.
    10.1074/jbc.M103232200
  112. Mendes, J.; Baptista, A.M.; Carrondo, M.A.; Soares, C.M.. "Implicit solvation in the self-consistent mean field theory method: Sidechain modelling and prediction of folding free energies of protein mutants". Journal of Computer-Aided Molecular Design 15 8 (2001): 721-740. http://www.scopus.com/inward/record.url?eid=2-s2.0-0034748018&partnerID=MN8TOARS.
    10.1023/A:1012279810260
  113. Mendes, J.; Nagarajaram, H.A.; Soares, C.M.; Blundell, T.L.; Carrondo, M.A.. "Incorporating knowledge-based biases into an energy-based side-chain modeling method: Application to comparative modeling of protein structure". Biopolymers 59 2 (2001): 72-86. http://www.scopus.com/inward/record.url?eid=2-s2.0-0034957437&partnerID=MN8TOARS.
    10.1002/1097-0282(200108)59:2<72::AID-BIP1007>3.0.CO;2-S
  114. Matias, P.M.; Soares, C.M.; Saraiva, L.M.; Coelho, R.; Morais, J.; Le Gall, J.; Carrondo, M.A.. "[NiFe] hydrogenase from Desulfovibrio desulfuricans ATCC 27774: Gene sequencing, three-dimensional structure determination and refinement at 1.8 Å and modelling studies of its interaction with the tetrahaem cytochrome c3". Journal of Biological Inorganic Chemistry 6 1 (2001): 63-81. http://www.scopus.com/inward/record.url?eid=2-s2.0-0034846760&partnerID=MN8TOARS.
    10.1007/s007750000167
  115. Baptista, A.M.; Scares, C.M.. "Some theoretical and computational aspects of the inclusion of proton isomerism in the protonation equilibrium of proteins". Journal of Physical Chemistry B 105 1 (2001): 293-309. http://www.scopus.com/inward/record.url?eid=2-s2.0-0035120969&partnerID=MN8TOARS.
  116. Power, D.M.; Elias, N.P.; Richardson, S.J.; Mendes, J.; Soares, C.M.; Santos, C.R.A.. "Evolution of the thyroid hormone-binding protein, transthyretin". General and Comparative Endocrinology 119 3 (2000): 241-255. http://www.scopus.com/inward/record.url?eid=2-s2.0-0033760484&partnerID=MN8TOARS.
    10.1006/gcen.2000.7520
  117. Sadeghi, S.J.; Valetti, F.; Cunha, C.A.; Romão, M.J.; Soares, C.M.; Gilardi, G.. "Ionic strength dependence of the non-physiological electron transfer between flavodoxin and cytochrome C553 from D. vulgaris". Journal of Biological Inorganic Chemistry 5 6 (2000): 730-737. http://www.scopus.com/inward/record.url?eid=2-s2.0-0033748801&partnerID=MN8TOARS.
    10.1007/s007750000162
  118. Mendes, J.; Soares, C.M.; Carrondo, M.A.. "Improvement of side-chain modeling in proteins with the self-consistent mean field theory method based on an analysis of the factors influencing prediction". Biopolymers 50 2 (1999): 111-131. http://www.scopus.com/inward/record.url?eid=2-s2.0-0033042104&partnerID=MN8TOARS.
    10.1002/(SICI)1097-0282(199908)50:2<111::AID-BIP1>3.0.CO;2-N
  119. Matias, P.M.; Saraiva, L.M.; Soares, C.M.; Coelho, A.V.; LeGall, J.; Carrondo, M.A.. "Nine-haem cytochrome c from Desulfovibrio desulfuricans ATCC 27774: Primary sequence determination, crystallographic refinement at 1.8 and modelling studies of its interaction with the tetrahaem cytochrome c3". Journal of Biological Inorganic Chemistry 4 4 (1999): 478-494. http://www.scopus.com/inward/record.url?eid=2-s2.0-0032836538&partnerID=MN8TOARS.
    10.1007/s007750050334
  120. Cunha, C.A.; Romão, M.J.; Sadeghi, S.J.; Valetti, F.; Gilardi, G.; Soares, C.M.. "Effects of protein-protein interactions on electron transfer: Docking and electron transfer calculations for complexes between flavodoxin and c- type cytochromes". Journal of Biological Inorganic Chemistry 4 3 (1999): 360-374. http://www.scopus.com/inward/record.url?eid=2-s2.0-0032788471&partnerID=MN8TOARS.
    10.1007/s007750050323
  121. Martel, P.J.; Soares, C.M.; Baptista, A.M.; Fuxreiter, M.; Náray-Szabó, G.; Louro, R.O.; Carrondo, M.A.. "Comparative redox and pK(a) calculations on cytochrome c3 from several Desulfovibrio species using continuum electrostatic methods". Journal of Biological Inorganic Chemistry 4 1 (1999): 73-86. http://www.scopus.com/inward/record.url?eid=2-s2.0-0032588946&partnerID=MN8TOARS.
    10.1007/s007750050291
  122. Mendes, J.; Baptista, A.M.; Carrondo, M.A.; Soares, C.M.. "Improved modeling of side-chains in proteins with rotamer-based methods: A flexible rotamer model". Proteins: Structure, Function and Genetics 37 4 (1999): 530-543. http://www.scopus.com/inward/record.url?eid=2-s2.0-0032732306&partnerID=MN8TOARS.
    10.1002/(SICI)1097-0134(19991201)37:4<530::AID-PROT4>3.0.CO;2-H
  123. Pereira, M.M.; Santana, M.; Soares, C.M.; Mendes, J.; Carita, J.N.; Fernandes, A.S.; Saraste, M.; Carrondo, M.A.; Teixeira, M.. "The caa3 terminal oxidase of the thermohalophilic bacterium Rhodothermus marinus: A HiPIP:oxygen oxidoreductase lacking the key glutamate of the D-channel". Biochimica et Biophysica Acta - Bioenergetics 1413 1 (1999): 1-13. http://www.scopus.com/inward/record.url?eid=2-s2.0-0032778747&partnerID=MN8TOARS.
    10.1016/S0005-2728(99)00073-0
  124. Frazão, C.; Bento, I.; Costa, J.; Soares, C.M.; Veríssimo, P.; Faro, C.; Pires, E.; Cooper, J.; Carrondo, M.A.. "Crystal structure of cardosin A, a glycosylated and Arg-Gly-Asp- containing aspartic proteinase from the flowers of Cynara cardunculus L.". Journal of Biological Chemistry 274 39 (1999): 27694-27701. http://www.scopus.com/inward/record.url?eid=2-s2.0-0033600810&partnerID=MN8TOARS.
    10.1074/jbc.274.39.27694
  125. Baptista, A.M.; Martel, P.J.; Soares, C.M.. "Simulation of electron-proton coupling with a Monte Carlo method: Application to cytochrome c3 using continuum electrostatics". Biophysical Journal 76 6 (1999): 2978-2998. http://www.scopus.com/inward/record.url?eid=2-s2.0-0033001692&partnerID=MN8TOARS.
    10.1016/S0006-3495(99)77452-7
  126. Petukhov, M.; Cregut, D.; Soares, C.M.; Serrano, L.. "Local water bridges and protein conformational stability". Protein Science 8 10 (1999): 1982-1989. http://www.scopus.com/inward/record.url?eid=2-s2.0-0032860932&partnerID=MN8TOARS.
  127. Burke, David F.; Deane, Charlotte M.; Nagarajaram, Hampapathalu A.; Campillo, Nuria; Martin-Martinez, Mercedes; Mendes, Joaquim; Molina, Franck; et al. "An iterative structure-assisted approach to sequence alignment and comparative modeling". Proteins: Structure, Function, and Genetics 37 S3 (1999): 55-60. http://dx.doi.org/10.1002/(sici)1097-0134(1999)37:3+<55::aid-prot8>3.0.co;2-b.
    10.1002/(sici)1097-0134(1999)37:3+<55::aid-prot8>3.0.co;2-b
  128. Fontes, N.; Conceição Almeida, M.; Peres, C.; Garcia, S.; Grave, J.; Aires-Barros, M.R.; Soares, C.M.; et al. "Cutinase activity and enantioselectivity in supercritical fluids". Industrial and Engineering Chemistry Research 37 8 (1998): 3189-3194. http://www.scopus.com/inward/record.url?eid=2-s2.0-3242794546&partnerID=MN8TOARS.
  129. Soares, C.M.; Martel, P.J.; Mendes, J.; Carrondo, M.A.. "Molecular dynamics simulation of cytochrome c3: Studying the reduction processes using free energy calculations". Biophysical Journal 74 4 (1998): 1708-1721. http://www.scopus.com/inward/record.url?eid=2-s2.0-0031892940&partnerID=MN8TOARS.
    10.1016/S0006-3495(98)77882-8
  130. Soares, C.M.; Martel, P.J.; Carrondo, M.A.. "Theoretical studies on the redox-Bohr effect in cytochrome c3 from Desulfovibrio vulgaris Hildenborough". Journal of Biological Inorganic Chemistry 2 6 (1997): 714-727. http://www.scopus.com/inward/record.url?eid=2-s2.0-0031458937&partnerID=MN8TOARS.
    10.1007/s007750050188
  131. Soares, C. M.; Björkstén, J.; Tapia, O.. "Perturbation-Relaxation Molecular Dynamics Simulations as a Tool to Explore Conformational Space. Reversible Response of the L3 Loop in Porin Towards Charge Screening Effects". Molecular Simulation 15 1 (1995): 35-46. http://dx.doi.org/10.1080/08927029508022327.
    10.1080/08927029508022327
  132. Stamato, F.M.L.G.; Paulino, M.; Garratt, R.; Soares, C.M.; Tapia, O.. "Computer assisted simulations and molecular graphics methods in molecular design 2. Proteinases and receptor and transport proteins". Molecular Engineering 4 4 (1995): 375-414. http://www.scopus.com/inward/record.url?eid=2-s2.0-0346376894&partnerID=MN8TOARS.
    10.1007/BF01019470
  133. Soares, C.M.; Bjorksten, J.; Tapia, O.. "L3 loop-mediated mechanisms of pore closing in porin: A molecular dynamics perturbation approach". Protein Engineering 8 1 (1995): 5-12. http://www.scopus.com/inward/record.url?eid=2-s2.0-0028939947&partnerID=MN8TOARS.
  134. Frazão, C.; Soares, C.M.; Carrondo, M.A.; Pohl, E.; Dauter, Z.; Wilson, K.S.; Hervés, M.; et al. "Ab initio determination of the crystal structure of cytochrome c6 and comparison with plastocyanin". Structure 3 11 (1995): 1159-1169. http://www.scopus.com/inward/record.url?eid=2-s2.0-13244252497&partnerID=MN8TOARS.
    10.1016/S0969-2126(01)00252-0
  135. Soares, C.M.; Tapia, O.. "Computer assisted simulations and molecular graphics methods in molecular design - 3. Methods based on statistical mechanics procedures". Molecular Engineering 4 4 (1995): 415-430. http://www.scopus.com/inward/record.url?eid=2-s2.0-34249766074&partnerID=MN8TOARS.
    10.1007/BF01019471
  136. Björkstén, J.; Soares, C.M.; Nilsson, O.; Tapia, O.. "On the stability and plastic properties of the interior l3 loop in R.capsulatus porin. A molecular dynamics study". Protein Engineering, Design and Selection 7 4 (1994): 487-493. http://www.scopus.com/inward/record.url?eid=2-s2.0-0028269774&partnerID=MN8TOARS.
    10.1093/protein/7.4.487
Capítulo de livro
  1. Bento, I.; Louro, RO; Soares, Claudio M.; Carrondo, MA. "Tetraheme cytochromes c3". In Handbook on Metalloproteins, editado por john wiley, 5-15. CRC Press, 2011.
  2. I Bento; Maria Arménia Carrondo; Claudio M. Soares; Ricardo Louro. "Tetraheme cytochromes C". editado por A. Messerschmidt, 5-15. John Wiley & Sons, 2011.
  3. Carrondo, M.A.; Soares, Claudio M.; Matias, PM. "Nine-heme cytochrome c". In Handbook on Metalloproteins. CRC Press, 2001.
Livro
  1. Lousa, D.; Baptista, A.M.; Soares, C.M.. Hydration effects on enzyme properties in nonaqueous media analyzed by MD simulations. 2016.
    10.4032/9789814669337
  2. Fontes, N.; Almeida, M.C.; Garcia, S.; Peres, C.; Grave, J.; Aires-Barros, M.R.; Soares, C.M.; et al. Cutinase activity and enantioselectivity in supercritical fluids. 1998.
    10.1016/S0921-0423(98)80072-5
Poster em conferência
  1. Teixeira, Rita I.; Buga, Carolina C.; Silva, Diogo H.; Moreira, Pedro; Cruz-Oliveira, Christine; Cruz-Oliveira, C.; Oliveira, C. C.; Veiga, Ana S.; Castanho, Miguel A. R. B.; et al. "Validating computational designed miniproteins for SARS-CoV-2 Spike Protein with Molecular Dynamics". Trabalho apresentado em Mini-symposium on Computational Biophysics: From Machine Learning to Coarse-Grained Simulations, 2025.
  2. Parada, Mariana; Luís, Inês M.; Sousa, Pedro; Buga, Ana Carolina; Veiga, Ana Salomé; Melo, Manuel N.; Soares, Claudio M.; et al. "Soluble ACE2 as a decoy for SARS-CoV-2". Trabalho apresentado em NOVAHealth Conference: Tackling Pandemics: Strategies for Prevention, Preparedness and Response, 2024.
  3. Moreira, Pedro; Shuhao Xiao; Madalena C. Marques; Mariana Parada; Carlota J. B. Conceição; Manuel N. Melo; Miguel Rocha; et al. "Development of a Computational Pipeline for the Design of Monobody Binders". Trabalho apresentado em FEBS3+ Meeting, 2024.
  4. Teixeira, Rita; Fernandes, Bárbara C; Cruz, Carlos; Parreiras, Susana; Buga, Carolina C.; Cruz-Oliveira, Christine; Cruz-Oliveira, C.; Oliveira, C. C.; Veiga, Ana S.; et al. "Computational design and validation of ACE2-based inhibitors against SARS-CoV-2". Trabalho apresentado em European South Athlantic Biophysics Congress, 2024.
  5. Diana Andreia Pereira Lousa; Moreira, Pedro; Carlos H. Cruz; Teixeira, Rita I.; Bárbara Fernandes; Buga, Carolina C.; Mariana Parada; et al. "Tailor made antiviral biopharmaceuticals design to experimental validation.". Trabalho apresentado em European South Atlantic Biophysics Congress, 2024.
  6. André Rafael Salgueiro; Moreira, Pedro; Diana Andreia Pereira Lousa; Soares, Claudio M.; Vanneschi, Leonardo. "Leveraging AI for the Design of Antibody-like Engineered Protein Scaffolds". Trabalho apresentado em Biophysics Festival – 4th Meeting of Young Biophysicists, Covilhã, Portugal, 9-10 May, 2024.
  7. Correia, João; Ferreira, Sofia; Rocha, Isabel; Lousa, Diana; Souza, Caio S.; Soares, Claudio M.. "A Computational Pipeline To Automate Gene Discovery and Enzyme Engineering". Trabalho apresentado em 4rd Meeting of Young Biophysicists "Biophysics Festival 2024", 2024.
  8. André R. F. Salgueiro; Moreira, Pedro; Soares, Claudio M.; Leonardo Vanescchi; Diana Andreia Pereira Lousa. "Artificial Intelligence-Based Design of Antibody-like Engineered Protein Scaffolds". Trabalho apresentado em Bioinformatic Open Days 2024, 2024.
  9. Diogo Silva; Moreira, Pedro; Teixeira, Rita I.; Bárbara Fernandes; Mariana Parada; Vicente, João B.; Diana Andreia Pereira Lousa; Soares, Claudio M.. "Addressing the challenge of oligomerization in computational protein design". Trabalho apresentado em Bioinformatics Open Days 2024, 2024.
  10. Madalena C. Marques; Moreira, Pedro; Teixeira, Rita I.; Marta Alenquer ; Maria João Amorim; Soares, Claudio M.; Vicente, João B.; Diana Andreia Pereira Lousa. "Antiviral proteins targeting Influenza A hemagglutinin: design, production and characterization". Trabalho apresentado em Bioinformatics Open Days 2024, 2024.
  11. Maria Benedita Pereira; Moreira, Pedro; Teixeira, Rita I.; Soares, Claudio M.; Diana Andreia Pereira Lousa. "Computational design of antiviral biologics targeting Zika virus envelope protein". Trabalho apresentado em Bioinformatics Open Days 2024, 2024.
  12. Madalena C. Marques; Moreira, Pedro; Parada, Mariana; Alenquer, Marta; Amorim, Maria João; Soares, Claudio M.; Lousa, Diana; Vicente, João B.. "Computational design and experimental validation of antiviral biologics targeting influenza A hemagglutinin". Trabalho apresentado em NOVAHealth Conference: Tackling Pandemics: Strategies for Prevention, Preparedness and Response, 2024.
  13. Teixeira, Rita I.; Valério, Mariana; Borges-Araújo, Luis; Manuel N. Melo; Vicente, João B.; Lousa, Diana; Soares, Claudio M.. "Probing the RBD-ACE2 interactions to unlock the design of biologics against SARS-CoV-2 variants". Trabalho apresentado em PEGS Europe: Protein & Antibody Engineering Summit, 2023.
  14. Moreira, Pedro; Parada, Mariana; Fernandes, Bárbara; Buckley, Stephen Michael; Georgeon, Sandrine ; Miguel Rocha; Vicente, João; et al. "Computational design of miniproteins to target SARS-CoV-2 RBD". 2023.
  15. Buga, Ana Carolina; Valério, Mariana; Soares, Claudio M.; Castanho, Miguel A. R. B.; Lousa, Diana; Ana Salomé Veiga. "Molecular insights into membrane fusion mediated by the parainfluenza fusion peptide". Trabalho apresentado em EMBO Workshop - Mechanisms of membrane fusion, 2023.
  16. Fernandes, Bárbara C; Pedro Moreira; Manuel N Melo; Soares, Claudio M.; Lousa, Diana; Vicente, João B.. "Computationally designed antiviral proteins targeting SARS-CoV-2 spike protein". Trabalho apresentado em BIOPHYSICS FESTIVAL - 3rd Meeting of Young Biophysicists, 2023.
  17. Parada, Mariana; Moreira, Pedro; Buga, Ana Carolina; Castanho, Miguel A. R. B.; Soares, Claudio M.; Melo, Manuel N.; Lousa, Diana; Veiga, Ana Salomé; Vicente, João B.. Autor correspondente: Moreira, Pedro. "Developing antivirals for the future". Trabalho apresentado em 3rd Meeting of Young Biophysicists, 2023.
  18. Correia, João; Caio S. Souza; Migle A. Bartels; Ferreira, Sofia; Lousa, Diana; Rocha, Isabel; Soares, Claudio M.. "Improving phenylalanine hydroxylase catalytic activity for tryptophan using an automated platform of structure-based enzyme engineering". Trabalho apresentado em Bioinformatics Open Days 2023, 2023.
  19. Saramago, Margarida; Bárria, Cátia; Costa, Vanessa G; Costa, Susana M.; Souza, Caio S.; Viegas, Sandra C.; Domingues, Susana; et al. "Biochemical characterization of SARS-CoV-2 nsp14-nsp10 complex: a promising target for drug design". Trabalho apresentado em IUBMB-FEBS-PABMB 2022 The Biochemistry Global Summit, 2022.
  20. Parreiras, Susana; Cruz, Carlos H.; Valério, Mariana; Sousa, Pedro M. F.; Soares, Claudio M.; Vicente, João B.; Lousa, Diana. Autor correspondente: Parreiras, Susana. "Design, production and characterization of antiviral proteins targeting SARS-CoV-2". Trabalho apresentado em The Biochemistry Global Summit Lisbon, 2022.
  21. Fernandes, Bárbara C.; Cruz, Carlos H.; Parreiras, Susana; Silva, Elísio; Soares, Claudio M.; Melo, Manuel N.; Lousa, Diana; Vicente, João B.. Autor correspondente: Fernandes, Bárbara C.. "Engineered proteins targeting SARS-CoV-2". Trabalho apresentado em 2nd Portuguese Young Biophysicists' Meeting, 2022.
  22. Teixeira, Rita I.; Valério, Mariana; Borges-Araújo, Luis; Manuel N. Melo; Vicente, João B.; Lousa, Diana; Soares, Claudio M.. Autor correspondente: Lousa, Diana. "The impact of SARS-CoV-2 Omicron variant on the human ACE2 binding: a computational study". Trabalho apresentado em 2nd Portuguese Young Biophysicists¿ Meeting, Biophysics Festival 2022,, 2022.
  23. Moreira, Pedro; Parada, Mariana; Vicente, João B.; Soares, Claudio M.; Rocha, Miguel; Lousa, Diana. "De novo antibody design targeting SARS-CoV-2 BA.5 RBD". Trabalho apresentado em V International Conference NOVA health Chronic Disease and Infection, 2022.
  24. Parreiras, Susana; Cruz, Carlos H.; Valério, Mariana; Sousa, Pedro M. F.; Soares, Claudio M.; Vicente, João B.; Lousa, Diana. Autor correspondente: Parreiras, Susana. "Design and production of antiviral proteins targeting SARS-CoV-2". Trabalho apresentado em 8th Meeting of Young Researchers in Computational Structural Biology 2021, 2021.
  25. Buga, Carolina C.; Valério, Mariana; Mendonça, Diogo A.; Vicente, João; Castanho, Miguel; Soares, Claudio M.; Veiga, Ana S.; Lousa, Diana. "Molecular determinants of SARS-CoV-2 fusion peptide activity". Trabalho apresentado em VIII Encontro de Jovens Investigadores em Biologia Computacional Estrutural, Coimbra, 2021.
  26. Cruz, Carlos; Buga, Carolina C.; Kosack, Lindsay; Alenquer, Marta; Demengeot, Jocelyne ; Amorim, Maria Joao; Soares, Claudio M.; Vicente, João B.; Lousa, Diana. "Antibodies elicited by rationally-designed FP-based immunogenic protein have high-affinity for the SARS-CoV-2 spike protein". Trabalho apresentado em VIII Encontro de Jovens Investigadores em Biologia Computacional Estrutural, Coimbra, 2021.
  27. Parreiras, Susana; Cruz, Carlos H.; Valério, Mariana; Soares, Claudio M.; Vicente, João B.; Lousa, Diana. Autor correspondente: Parreiras, Susana. "Rationally designed antiviral proteins targeting SARS-CoV-2". Trabalho apresentado em 10th edition of Bioinformatics Open Days 2021, 2021.
  28. M. Paquete, Catarina; Fonseca, Bruno M; Cruz, David E; Pereira, Tiago; Pacheco, Isabel; Soares, Claudio M.; Louro, Ricardo. "Exploring the molecular interactions responsible for indirect electron transfer in Shewanella oneidensis MR-1". Trabalho apresentado em 2nd European International Society for Microbial Electrochemistry and Technology Meeting, 2014.
  29. Fonseca, Bruno M; Saraiva, Ivo H; M. Paquete, Catarina; Soares, Claudio M.; Pacheco, Isabel; Salgueiro, Carlos A.; Louro, Ricardo. "Thermodynamic bias for functional specificity of the different hemes of the small tetraheme cytochrome c from Shewanella oneidensis". Trabalho apresentado em IV Bienal of NMR, 2008.
Resumo em conferência
  1. Moreira, Pedro; Shuhao Xiao; Ye Wei; Joseph Schimdt; Mariana Parada; Carlota J. B. Conceição; Miguel Rocha; et al. "Computational design of monobody binders to target viral therapeutical epitopes". Trabalho apresentado em 3D-Biodata-PT (3rd Annual Meeting), Lisboa, 2024.
    Aceite para publicação
  2. Madalena C. Marques; Moreira, Pedro; Teixeira, Rita I.; Marta Alenquer ; Maria João Amorim; Soares, Claudio M.; Vicente, João B.; Diana Andreia Pereira Lousa. "Combining computational and experimental methods to develop tailor-made biopharmaceuticals targeting Influenza A Hemagglutinin (Flash Talk).". Trabalho apresentado em Biophysics Festival – 4th Meeting of Young Biophysicists, Covilhã, 2024.
    Aceite para publicação
  3. Maria Benedita Pereira; Moreira, Pedro; Teixeira, Rita I.; Diana Andreia Pereira Lousa; Soares, Claudio M.. "Computational design of novel antivirals that target the Zika virus Envelope protein domain III (Flash Talk)". Trabalho apresentado em Biophysics Festival – 4th Meeting of Young Biophysicists, Covilhã, 2024.
    Aceite para publicação
  4. Buga, Carolina C.; Valério, Mariana; Castanho, Miguel A.R.B. ; Soares, Claudio M.; Ana Salomé Veiga; Lousa, Diana. "Unveiling the molecular mechanism of membrane fusion mediated by the parainfluenza fusion peptide". Trabalho apresentado em European Biophysical Societies' Association (EBSA) congress 2023, stockholm, 2023.
  5. Buga, Carolina C.; Valério, Mariana; Mendonça, Diogo A.; Vicente, João B.; Castanho, Miguel A. R. B.; Soares, Claudio M.; Lousa, Diana; Veiga, Ana S.. "Molecular determinants of the SARS-CoV-2 fusion peptide activity". Trabalho apresentado em 25thIUBMB-46thFEBS-15thPABMB Congress, Lisbon, 2022.
    Aceite para publicação
  6. Fonseca, Bruno M; M. Paquete, Catarina; Neto, Sónia E; Cruz, David; Pacheco, Isabel; Soares, Claudio M.; Louro, Ricardo. "Molecular details of indirect extracellular electron transfer between bacteria and metallic solids or electrodes". 2014.
    Publicado
  7. Cruz, David ; Castro, Tarsila Gabriel; Soares, Claudio M.; Micaêlo, Nuno M.. "Structure-based design of antimicrobial peptaibols bearing unnatural a,a-dialkylglycines". 2013.
    10.1007/s00249-013-0917-x
  8. Campos, Elisa J.; Asandei, Alina; McVey, Colin E.; dias, joão carlos; oliveira, asf; Soares, Claudio M.; Luchian, Tudor; Astier, Yann. "Sensing modified-gold nanoparticles with the a-hemolysin pore". Trabalho apresentado em 9th International Conference on Nanosciences & Nanotechnologies (NN12), Thessaloniki, 2012.
    Publicado

Outros

Outra produção
  1. Editorial. Computational Approaches to Foster Innovation in the Treatment and Diagnosis of Infectious Diseases. 2022. Diana Lousa; Claudio M. Soares; Fernando L. Barroso da Silva. https://novaresearch.unl.pt/en/publications/43844e17-ae22-4479-b86c-6d58386d5c34.
    10.3389/fmedt.2022.841088
  2. SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessibility. 2021. Mariana Valério; Luís Borges-Araújo; Manuel N. Melo; Diana Lousa; Cláudio M. Soares. https://doi.org/10.1101/2021.11.30.470470.
    10.1101/2021.11.30.470470
Atividades

Apresentação oral de trabalho

Título da apresentação Nome do evento
Anfitrião (Local do evento)
2021/12 Lousa D, Valério M, Buga CC, Sequeira A, Victor BL, Laio A, Mendonça DA, Morais J, Melo MN, Rocha M, Castanho MARB, Veiga AS, Soares CM (2021) “Viral membrane fusion: characterizing and inactivating a crucial step of the infection by devastating pathogens.”, Invited oral presentation by D. Lousa in the EJIBCE 2021, Coimbra, Portugal, 20 December 2021 EJIBCE 2021
EJIBCE 2021 (Coimbra, Portugal)
2021/12 Araújo LB, Valério MF, Melo MN, Lousa D, Soares CM (2021), “SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessibility.” Selected oral presentation by LB Araújo in the EJIBCE 2021, Coimbra, Portugal, 20 December 2021 EJIBCE 2021
EJIBCE 2021 (Coimbra, Portugal)
2021/12 Cruz C, Buga CC, Parreiras S, Valério M, Soares CM, Vicente JB and Lousa D (2021). “Protein Engineering of Mini Therapeutic Proteins against SARS-CoV-2”. Selected oral presentation in the 10th Bioinformatics Open Days – online meeting, Braga, Portugal, 5-8 May 2021 10th Bioinformatics Open Days
10th Bioinformatics Open Days (Braga, Portugal)
2021/12 Valério MF, Mendonça D, Morais J, Cruz CH, Castanho MARB, Veiga AS, Melo MN, Soares CM, Lousa D (2021) “Parainfluenza fusion peptide promotes membrane fusion by assembling into oligomeric pore-like structures.” Selected oral presentation by MF Valério in the EJIBCE 2021, Coimbra, Portugal, 20 December 2021 EJIBCE 2021
EJIBCE 2021 (Coimbra, Portugal)
2021/04 Valério MF, Mendonça D, Morais J, Cruz CH, Castanho MARB, Veiga AS, Melo MN, Soares CM, Lousa D (2021) “Parainfluenza Fusion Peptide Forms Oligomeric Pore-like Structures Inside A Membrane”. Selected oral presentation by MF Valério 7th European Joint Theoretical/Experimental Meeting on Membranes – online meeting
(Graz, Áustria)
2019/07 D. Lousa, A.R.T. Pinto, S.R.R. Campos, A.M. Baptista, A.S. Veiga, M.A.R.B. Castanho, C.M. Soares. “Effect of pH on the influenza fusion peptide structure and activity: A constant-pH molecular dynamics approach”. Selected oral presentation by D. Lousa in JOINT 12th EBSA congress, 10th ICBP - IUPAP congress, Madrid, Spain
(Madrid, Espanha)
2019/02/02 Characterizing the influenza virus fusion machinery: A computational approach JORTEC Bioquímca 2019
FCT NOVA, Portugal (Caparica, Portugal)
2018/10/12 Abreu, B, Soares, CM (2018) "Unveiling the role of the mutation F508del in cystic fibrosis" Oral communication (by B. Abreu) in the Lisbon Biophysics Networking Meeting: From Protein Dynamics to Membrane Biophysics: Instituto Superior Técnico, Portugal
(Lisboa, Portugal)
2018/10 Velada, I, Cardoso, H, Grzebelus, D, Lousa, D, Soares, CM, Macedo, ES, Arnholdt-Schmitt, B, Peixe, A (2018) “IBA-induced in vitro adventitious rooting in olive: a molecular response to cut injury and auxin application”. Selected oral presentation by I Velada in the Olive Bioteq 18, Seville, Spain
(Sevilha, Espanha)
2018/05 Lousa, D, Pinto, ART, Victor, BL, Laio, A, Veiga, AS, Castanho, MARB, Soares, CM (2018) “Molecular properties of the influenza fusion peptide: Combining simulation and experiment”. Invited talk at the 47th Annual Meeting of the Brazilian Society for Biochemistry and Molecular Biology, Joinville, Brazil
(Joinville, Brasil)
2016/09 Soares, CM (2016) “MD Simulation of Biological Systems: from Enzymes to (other) Molecular Machines”. Invited talk at the 2016 Summer School in Computational Biology, Coimbra (Portugal)
(Coimbra, Portugal)
2016/07 Baptista, A. M., Oliveira, A. S., Campos, S. R. R., Magalhães, P. R., Soares C. M. (2016) "Couplings Involving Protonation and Conformation in Cytochrome c Oxidase: Insights from Constant-pH MD and PB/MC Simulations". Invited talk by AM Baptista at "Protein Electrostatics Berlin 2016", Berlin, Germany
(Berlim, Alemanha)
2016/06 Lousa, D., Pinto A. R. T., Veiga A. S., Laio A., Castanho M. A. R. B. Castanho and Soares C. M., "Structure and activity of the influenza fusion peptide: a combined simulation and experimental approach", selected oral presentation by D. Lousa in 5th International Iberian Biophysics Congress, Porto, Portugal
(Porto, Portugal)
2016/06 Oliveira, ASF, Campos, SRR, Baptista, AM, Soares, CM (2015) “Coupling between protonation and conformation in cytochrome c oxidase: Insights from constant-pH MD simulations”, selected oral presentation by ASF Oliveira in 5th International Iberian Biophysics Congress, Porto, Portugal
(Porto, Portugal)
2016/02 Lousa D., Pinto A. R. T., Veiga A. S., Laio A., Castanho M. A. R. B. Castanho and Soares C. M., "When simulation and experiment fuse: Analysing the interaction of the influenza fusion peptide with model membranes", selected oral presentation by D. Lousa in XV Iberic Peptide Meeting, Porto, Portugal
(Porto, Portugal)
2015/12/18 Oliveira, ASF, Campos, SRR, Baptista, AM, Soares, CM (2015) “Unraveling the coupling between protonation and conformation: Constant-pH MD simulations of Cytochrome c oxidase”. Oral presentation by ASF Oliveira at 3rd EJIBCE meeting held in Coimbra, Portugal
(Coimbra, Portugal)
2015/12/18 Lousa D., Pinto A. R. T., Veiga A. S., Laio A., Castanho M. A. R. B. Castanho and Soares C. M., "When simulation and experiment fuse: Analysing the interaction of the influenza fusion peptide with model membranes", selected oral presentation by D. Lousa in EJIBCE III, Coimbra, Portugal
(Coimbra, Portugal)
2015/08 Campos, S. R. R., Oliveira, A. S. F., Magalhães, P. R., Vila-Viçosa, D., Teixeira, V. H., Santos, H. A. F., Soares, C. M., Machuqueiro, M., Baptista, A. M. (2015) "Constant- pH molecular dynamics simulations of membrane systems: titrable lipids and proton pumps". Invited talk by A. M. Baptista at 250th American Chemical Society National Meeting, Boston MA, USA,
(Boston, Portugal)
2015/07 Baptista, A. M., Oliveira, A. S. F., Campos, S. R. R., Magalhães, P. R., Soares, C. M. (2015) "Constant-pH MD of cytochrome c oxidase". Invited talk by A. M. Baptista at Workshop on Protein Electrostatics, Telluride Science Research Center, Telluride CO, USA
(Coloride, Estados Unidos)
2015/01/22 Soares, CM (2015) “Structural bioinformatics towards the understanding of the molecular machines of life” Invited seminar held at Universidade do Minho
(Braga, Portugal)
2014/12 Damas, JM, Baptista, AM, Soares, CM “A new pathway for O2 diffusion inside laccases and multicopper oxidases”, Oral presentation by JM Damas at the EJIBCE II, Lisboa, Portugal
(Lisboa, Portugal)
2014/08 Damas, JM, Baltazar, CSA, Teixeira VH, Baptista, AM, Soares, CM (2014) “Modelling of important redox enzymes in biotechnology: laccases and hydrogenases”. Invited seminar in the conference “Molecular Modelling 2014: From biomolecules to materials”, Lamington National Park, Queensland, Australia
(Queensland, Austrália)
2014/08 Lousa, D, Victor, BL, Antunes, J, Soares, CM (2014) “Molecular dynamics simulation studies of the interaction of influenza hemagglutinin fusion peptide with membranes”. Invited seminar in “2014 IUPAB International Biophysics Congress”, Brisbane, Australia
(Brisbane, Austrália)
2014/08 Lousa D.; Victor B. L., Fernandez C. and Soares C. M., “Molecular insights into the role of the fusion peptide from influenza virus: A computational analysis”, selected oral presentation by D. Lousa in FEBS Young Scientists’ Forum, Paris
(Paris, França)
2014/08 Damas, JM, Bento, I, Silva, CS, Chen, Z, Brissos, V, Martins, LO, Lindley, PF, Baptista, AM, Soares, CM (2014) “Molecular Mechanisms in laccases: insights from structural and simulation studies”. Plenary Lecture in the 4th International Conference on Novel Enzymes
(Ghent, Bélgica)
2014/06/30 Damas, JM, Baltazar, CSA, Teixeira, VH, Baptista, AM, Soares, CM (2014) “Redox enzymes for biotechnology: modelling (and other) studies of laccases and hydrogenases”. Invited seminar in the SFB – Protonation dynamics in protein function, held in the Freie Universität, Berlin, Germany
(Berlin, Alemanha)
2014/05 Lousa, D, Victor, BL, Demmelhuber, L, Baptista, AM, Soares, CM (2014) “Interaction of Influenza hemagglutinin with membranes: a molecular dynamics analysis” Invited Conference held in XLIII Annual Meeting of the SBBq (The Brasilian Society for Biochemistry and Molecular Biology) held at Foz do Iguaçu, Paraná, Brazil
(Paraná, Brasil)
2014/03/28 Soares, CM (2014) “Structural bioinformatics towards the understanding of the molecular machines of life” Invited seminar (Portuguese Biophysical Society Conference) held at Universidade do Algarve
(Algarve, Portugal)
2014/03 Lousa, D, Cianci, M, Helliwell, JR, Halling, PJ, Baptista, AM, Soares,CM (2014) “Simulation of proteins in nonaqueous media”. Invited oral presentation in the CECAM meeting “Biological Molecules under non-natural conditions”, Stuttgart, Germany
(Estugarda, Alemanha)
2014/03 Cianci, M, Tomaszewski, B, Lousa, D, Baptista, AM, Soares,CM, Helliwell, JR, Halling, PJ (2014) “Analysis of counter-ion effects in nonaqueous enzymology of subtilisin”. Invited oral presentation (by M. Cianci) in the CECAM meeting “Biological Molecules under non-natural conditions”, Stuttgart, Germany
(Estugarda, Alemanha)
2014/02 Baltazar, CSA, Teixeira, VH, Soares, CM (2014) “Understanding the special properties of [NiFeSe] hydrogenases through the use of computational methodologies”. Short Oral Presentation (by CSA Baltazar) in the Biophysical Society 58th Annual Meeting, San Francisco, California, USA
(California, Estados Unidos)
2013/11 Oliveira, ASF, Victor, BL, Lousa, D, Baltazar, CA, Rafael, P, Fernandez, C, Melo, R, Baptista, AM, Soares, CM (2013) “Simulation of Membrane Proteins”. Oral presentation in INSTRUCT and BioStruct-X course “Structure and Function of Membrane Proteins - a multidisciplinary approach”, ITQB-UNL, Oeiras, Portugal
(Oeiras, Portugal)
2013/07 Oliveira, ASF, Damas, JM, Baptista, AM, Soares, CM (2013) “Exploring the dioxygen diffusion pathways in aa3 cytochrome c oxidases: insights from MD simulations”. Short Oral Presentation (by ASF Oliveira) in the 9th EBSA European Biophysics Congress, Lisbon, Portugal
(Lisboa, Portugal)
2013/05/20 Soares, CM “Simulation of proteins in nonaqueous media: basic knowledge towards enzyme engineering”. Invited seminar held at Instituto Superior Técnico, Lisbon
(Lisboa, Portugal)
2013/05 Soares, CM, Oliveira, AS, Damas, JM, Baptista, AM. “Simulating molecular mechanisms of ABC transporters”. Invited Lecture in the 11º Encontro Nacional de Química-Física”, Porto, Portugal
(Porto, Portugal)
2012/09 Cianci, M, Tomaszewski, M, Lousa, D, Baptista, AM, Soares, CM, Helliwell, JR, Halling, PJ (2012) “Analysis of counter-ion effects in nonaqueous enzymology of subtilisin”. Oral presentation (by M. Cianci) on the 6th International Congress on Biocatalysis, Hamburg, Germany
(Hamburgo, Alemanha)
2012/07 E. Campos, A. Asandei, C.E. McVey, J. C. Dias, A.S.F. Oliveira, C.M. Soares, T. Luchian, Y. Astier. "Sensing modified-gold nanoparticles with the a-hemolysin pore". Oral presentation (by E. Campos) in the 9th International Conference on Nanosciences & Nanotechnologies (NN12), Thessaloniki, Greece
(Thessaloniki, Grécia)
2012/05/23 Soares, CM (2012) “Simulating enzymes in non-standard media: structure, dynamics and selectivity”. Invited seminar held at Centro de Química da Universidade de Évora
(Évora, Portugal)
2012/05 Soares, CM, Lousa, D, Micaelo, NM, Baptista, AM (2012) “Simulating the unusual properties of enzymes in nonaqueous media: basic knowledge approaching rational engineering”. Plenary lecture held at the International Conference “In silico enzyme design and screening”. Trieste, Italy
(Trieste, Itália)
2012/05 Soares, CM (2012) “Understanding molecules and life through the eyes of structural bioinformatics”. Invited seminar held at “Jornadas de Química e Bioquímica”, Universidade da Beira Interior, Covilhã
(Covilhã, Portugal)
2012/03 Soares, CM (2011) Structural bioinformatics towards the understanding of molecules and life”. Invited seminar held at the “Bioinformatics Open Days”, Universidade do Minho, Braga
(Braga, Portugal)
2011/10/14 Soares, CM, Oliveira, AS, Damas, JM, Baptista, AM (2011) “The power stroke in ABC transporters: insights from simulation.”, Invited seminar held at Instituto Gulbenkian de Ciência
(Oeiras, Portugal)
2011/09 Soares, CM, Oliveira, AS, Damas, JM, Baptista, AM (2011) “Molecular mechanisms of ABC transporters: a simulation approach”, Invited seminar in the XXXIV Congreso de la Sociedade Española de Bioquímica y Biología Molecular (34th Congress of the Spanish Biochemical and Molecular Biology Society), Barcelona, Spain
(Barcelona, Espanha)
2011/05 Soares, CM, Oliveira, AS, Damas, JM, Baptista, AM (2011) “Insights into the molecular mechanisms of ABC transporters”, Invited seminar in the INTERBIO Symposium “Frontiers in Protein Research, ITQB-UNL, Oeiras, Portugal
(Oeiras, Portugal)
2011/03/30 Soares, CM (2011) “Do Computers Dream of Electric Molecules? Seeing life through biomolecular modelling”, Invited seminar held at Centro de Química e Bioquímica – Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
(Lisboa, Portugal)
2011/02/15 Soares, CM (2011) “Biomolecular modelling towards the understanding of Life at the molecular level”, Invited seminar held at Instituto de Higiene e Medicina Tropical – Universidade Nova de Lisboa, Lisbon, Portugal
(Lisboa, Portugal)
2010/11/25 Soares, CM (2010) “Life at the molecular level: contributions from biomolecular modelling / structural bioinformatics”, Invited seminar held at Instituto de Medicina Molecular – Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
(Lisboa, Portugal)
2010/04/12 Soares, CM (2010) “Protein Modelling Laboratory@ITQB-UNL”. Invited seminar in the INTERBIO workshop, ITQB-UNL, Oeiras, Portugal
(Oeiras, Portugal)
2010/04/12 Soares, CM (2010) “Protein Modelling Laboratory @ ITQB-UNL. (Recent) Past, present and (near) future”, Invited seminar held at Instituto Gulbenkian de Ciência
(Oeiras, Portugal)
2008/09 Soares, CM (2008) “Molecular modelling of hydrogenases”. Invited communication in the Workshop “Structure, dynamics, and function of proteins”, ITQB-UNL, Oeiras, Portugal
(Oeiras, Portugal)
2007/05 Soares, CM (2007) “Electron and proton transfer in redox proteins and redox chains. A modelling perspective”, Invited communication in the FEBS Workshop “Trends in transient interactions between biological macromolecules”- Seville, Spain
(Sevilha, Espanha)
2004/11/01 Victor, BL, Baptista, AM, Soares, CM (2004) “A new theoretical approach to study proton channels in the Quinol oxidase aa3 from Acidianus ambivalens”. Short oral presentation (by BL Victor) in the 3rd Portuguese-Spanish Biophysics Congress – Lisbon, Portugal
(Lisboa, Portugal)
2004/11 Soares, CM (2004) “Modelling enzymes for biotechnology applications”. Invited communication in the Cost Action 847 & D32 workshop - – Póvoa de Varzim, Portugal
(Póvoa de Varzim, Portugal)
2004/10/29 Micaelo, NM, Teixeira, VH, Baptista, AM, Soares, CM (2004) “Water dependent properties of cutinase in nonaqueous solvents”. Short oral presentation (by NM Micaelo) in the 3rd Portuguese-Spanish Biophysics Congress – Lisbon, Portugal
(Lisboa, Portugal)
2003/10 Soares, C.M. (2003) "Structural genomics: protein structure prediction". Seminar given in the 5th Short course of the Portuguese Biophysical Society "Genomics and Proteomics: biophysical perspectives" - Santarém, Portugal
(Caparica, Portugal)
2003/10 Soares, C.M. (2003) "Structural genomics: protein structure prediction". Seminar given in the 5th Short course of the Portuguese Biophysical Society "Genomics and Proteomics: biophysical perspectives"- Santarém, Portugal
(Santarém, Portugal)
2003/09 Soares, CM (2003) "Molecular dynamics simulations of proteins in nonaqueous solvents". Invited seminar in the "6º Encontro Nacional de Química-Física" - Lisbon, Portugal
(Lisboa, Portugal)
2003/06 Soares, CM (2003) "Protein modelling group @ ITQB. Biomolecular modelling / Structural bioinformatics". Seminar given at the "Oeiras mathematical and computational biology workshop" – Oeiras, Portugal
(Oeiras, Portugal)
2003/06 Martins, LO, Enguita, FJ, Pereira, MM, Teixeira, M, Costa, T, Soares, CM, Carrondo, MA, Henriques, AO (2003) "Biochemical and structural characterization of Bacillus subtilis spore coat protein CotA". Oral presentation (by LO Martins) in the Functional Genomics of Gram-positive Microorganisms" & "12th International Conference on Bacilli" - Baveno, Italy
(Baveno, Itália)
2003/04 Soares, CM (2003) "Modelação de proteínas/Bioinformática estrutural: perspectivas e aplicações". Seminar given at the "VI Jornadas de Engenharia Biológica da Universidade do Minho" – Gerês, Portugal
(Gerês, Portugal)
2003/04 Soares, CM (2003) "Da bioquímica à biofísica molecular. Uma visão mecanicista da vida". Seminar given at the "I Encontro Nacional de Estudantes de Bioquímica" – Coimbra, Portugal
(Oeiras, Portugal)
2003/02 Soares, CM (2003) "Modelling redox proteins: the molecular basis of electron and proton transfer". Seminar given at the Department of Biology, Universidade do Minho – Braga, Portugal
(Braga, Portugal)
2002/12 Martins, LO, Soares, CM, Pereira, MM, Teixeira, M, Costa, T, Enguita, FJ, Carrondo, MA, Henriques, AO (2002) "Studies in CotA, a laccase associated with the Bacillus subtilis spore coat". Oral presentation (by LO Martins) in the XIII Congresso Nacional de Bioquímica - Lisbon, Portugal
(Lisboa, Portugal)
2002/07 Jackson P, Price N, Soares C. (2002) "LEP1: an extensin peroxidase in lupin". Oral presentation (by P. Jackson) International Symposium of Plant peroxidases - Murcia, Spain
(Murcia, Espanha)
2002/04 Baptista, A.M., Soares, C.M. (2002) "Constant-pH molecular dynamics simulations using stochastic titration". Oral presentation (by A.M. Baptista) in the 223rd American Chemical Society National Meeting – Orlando, USA
(Orlando, Estados Unidos)
2002/04 Soares, C.M. (2002) "Transferência electrónica e protónica em proteínas: estudos de modelação molecular". Invited seminar in the Departamento de Química e Bioquímica, FCUL - Lisbon
(Lisboa, Portugal)
2002/01 Soares, C.M. (2002) "Molecular modelling studies on multi-haem cytochromes: methodological and biological aspects of electron and proton transfer". Invited seminar in the Competence Center for Computational Chemistry (C4) seminar program, ETH-Zurich – Zurich, Switzerland
(Zurique, Suiça)
2001/10 Soares, C.M. (2001) "Molecular dynamics simulation: beyond protein structure". Seminar given in the 3rd Short course of the Portuguese Biophysical Society "Proteins: from structure to dynamics" - Santarém, Portugal
(Santarém, Portugal)
2001/10 Soares, C.M., Baptista, A.M., Martel, P.J., Teixeira, V.H (2001) "Molecular modelling of redox proteins: from single molecules to redox chains". Seminar given in the in the IV Gulbenkian Autumn Meeting: Theoretical and computational Biology - Oeiras, Portugal
(Oeiras, Portugal)
2001/02 Soares, C.M. "Molecular modelling of electron and proton transfer in proteins". Seminar presented in the Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa - Monte de Caparica, Portugal
(Caparica, Portugal)
2001/01 Soares, C.M. "Modelação molecular de proteínas envolvidas em processos de oxidação-redução em bactérias redutoras de sulfato". Seminar presented in the Departamento de Química da Universidade do Minho, Braga
(Braga, Portugal)
2001/01 Soares, C.M. "Modelação molecular de proteínas: transferência electrónica e protónica em citocromos multihémicos". Seminar presented in the Centro de Física Computacional da Universidade de Coimbra - Coimbra, Portugal
(Coimbra, Portugal)
2000/09 Teixeira, V.H., Soares, C.M., Baptista, A.M. " Identification of the groups responsible for the Redox-Bohr effect in cytochromes c3 from various species: molecular modelling studies.". Oral presentation (by V.H. Teixeira) at the XII Congresso Nacional de Bioquímica - Póvoa de Varzim, Portugal
(Póvoa de Varzim, Portugal)
2000/07 Soares, C.M. (2000) "Electron and proton transfer in multihaem cytochromes: a modelling approach". Invited talk on the 5th European Biological Inorganic Chemistry Conference – Toulouse, France
(Toulouse, França)
2000/03 Soares, C.M. (2000) "Modelação molecular de biomoleculas". Seminar given in "Jornadas de Engenharia Biotecnologica" – Universidade do Algarve, Portugal
(Algarve, Portugal)
1999/10 Soares, C.M. (1999) "Theoretical aspects of molecular mechanics/dynamics simulation. Some applications". Seminar given in the 2nd Short course of the Portuguese Biophysical Society "Simulation of biological processes. Practical approaches" - Santarém, Portugal
(Santarém, Portugal)
1998/09 Soares, C.M., Martel, P.J., Baptista, A.M., Carrondo, M.A. “Molecular modelling studies in cytochromes c3“. Invited talk in the “ISQBP President’s Meeting: Molecular structure and dynamics in biology” - Elba, Italy
(Elba, Itália)
1998/09 Mendes, J., Soares, C.M., Carrondo, M.A. (1998) “Prediction of side chain conformation in proteins”. Seminar given (by J. Mendes) in the TMR Summer School “Structure and function of metalloproteins” – ITQB-UNL, Oeiras, Portugal
(Oeiras, Portugal)
1998/07 Soares, C.M. “Theoretical studies on tetraheme cytochromes c3”. Seminar given in the TMR Summer School “Spectroscopy and engineering of metalloproteins” – ITQB-UNL, Oeiras, Portugal
(Oeiras, Portugal)
1998/01 Soares, C.M. ”Electrostatic and molecular dynamics studies in cytochromes c3”. Seminar given in the Workshop on Structural Biology: Advances in X-Ray analysis, NMR, Modelling and Design - Cambridge University, UK
(Cambridge, Reino Unido)
1995/12 Soares, C.M., Martel, P.J., Carrondo, M.A. ”Molecular modelling studies of cytochrome c3”. Invited talk in the “1st Portuguese-Spanish Biophysics Congress” – Lisbon, Portugal
(Lisboa, Portugal)
1995/11 Soares, C.M. “Molecular modelling on electron transfer proteins. Some case studies”. Seminar given in the symposium “Protein Structure & Motion” – Barcelona, Spain
(Barcelona, Espanha)

Orientação

Título / Tema
Papel desempenhado
Curso (Tipo)
Instituição / Organização
2019/05 - Atual Computational enzyme engineering
Orientador
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2017/09 - Atual Metabolic Engineering aided by computer-guide enzyme engineering for the optimization of cell factories
Coorientador de Joana Filipa Azevedo Oliveira
Bioengenharia (Doutoramento)
Universidade do Minho, Portugal
2017/09 - Atual Viral Membrane Fusion: Structural determinants and dynamical behaviour
Orientador
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2016/01 - Atual The structural basis of substrate translocation in ABC transporters: a biomolecular simulation approach
Orientador
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2016/01 - Atual Efficient algorithms for protein docking
Coorientador
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Universidade de Lisboa Instituto Superior Técnico, Portugal
2016/01 - Atual Genome-scale modeling of allosteric regulation in E. coli
Coorientador
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Universidade do Minho, Portugal
2014/01 - Atual Membrane altering proteins: a computational study of viral membrane fusion and antimicrobial peptides
Orientador de Davide Ribeiro da Cruz
Bioquímica (Doutoramento)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2013/03 - Atual Molecular mechanisms of viral membrane fusion: A computational analysis
Orientador
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2008/01 - Atual Ligand interaction and binding in laccases – reduced substrates, dioxygen and protons
Orientador
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2018/03 - 2019/03 Structural and dynamic properties of the Dengue fusion peptide in a membrane bilayer: A computational approach
Coorientador
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2014/01 - 2018/12 Improving predictions in metabolic engineering problems by incorporating enzyme structural information
Coorientador de Tiago Filipe Coelho Resende
Bioengenharia (Doutoramento)
Universidade do Minho, Portugal
2016 - 2017/05 Exploring the Structural and dynamical properties of the dengue fusion peptide in a membrane bilayer using molecular simulation methods
Coorientador
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2011/03 - 2017/01 Studying proton transfer and proton pumping in Cytochrome c Oxidases: methodological developments and their application.
Orientador
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2011 - 2016/03 Modelação molecular/bioinformática estrutural da hemaglutinina do vírus influenza
Orientador de Jorge Miguel Penela Deus Antunes
Bioquímica (Mestrado)
Universidade de Lisboa Faculdade de Ciências, Portugal
2008 - 2012 Molecular mechanisms of membrane fusion in influenza virus
Orientador
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2008/10 - 2009/11 Estudo da difusão do hidrogénio molecular numa hidrogenase [NiFeSe] por métodos de dinâmica molecular
Orientador
Universidade de Lisboa Faculdade de Ciências, Portugal
2006/09 - 2007/10 Modelação molecular dos domínios de ligação de nucleótido de um transportador ABC
Orientador
Universidade de Lisboa Faculdade de Ciências, Portugal
2002/11 - 2007/02 Molecular Modelling of Redox Proteins Involved in the Hydrogen Metabolism
Orientador de Vítor Hugo Oliveira Teixeira
Bioquímica (Doutoramento)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2003/04 - 2007 Enzyme Structure and Function in Nonaqueous Solvents
Orientador de Nuno Miguel da Silva Micaêlo
Bioquímica (Doutoramento)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2003/03 - 2007 Molecular Modeling of Redox Proteins Involved in the Oxygen and Nitric Oxide Metabolism
Orientador de Bruno Lourenço da Silva Victor
Bioquímica (Doutoramento)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2003 - 2007 Methodological and computational developments for modeling protonation and redox processes in biological systems of relevant importance.
Orientador
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2006 - 2006 Molecular Modelling of Abc Transporters: from Atp Hydrolysis to Substrate Transport
Orientador de Ana Sofia Fernandes de Oliveira
Bioquímica (Doutoramento)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2006 - 2006 Molecular determinants of nonaqueous biocatalysis: A computational analysis
Orientador de Diana Andreia Pereira Lousa
Bioquímica (Doutoramento)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2004/09 - 2005/02 Criação de um sistema de computação distribuída para simulações moleculares
Orientador
2001 - 2003 Electrostatic studies in proteins
Orientador
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
1998 - 2003 The crystal structure of cytochrome c nitrite reductase from Desulfovibrio desulfuricans and modelling studies of electron transfer between flavodoxin and mono-heme cytochromes
Coorientador de Carlos Manuel Alves da Costa Cunha
Bioquímica (Doutoramento)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2000/09 - 2001/09 Modelação molecular da interacção de proteínas em Desulfovibrio gigas
Orientador
Universidade de Coimbra, Portugal
1998/09 - 2000/11 Modelação e estudos de docking na transtirretina de dourada, Sparus aurata
Orientador
Universidade do Algarve, Portugal
1999/09 - 2000/10 Estudo comparativo de propriedades de redução e protonação em citocromos c3 de várias espécies de bactérias redutoras de sulfato
Orientador
Universidade do Algarve, Portugal
2000 - 2000 Modelling Sidechain Conformations in Proteins
Coorientador de Joaquim Pires Antunes Mendes
Bioquímica (Doutoramento)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Organização de evento

Nome do evento
Tipo de evento (Tipo de participação)
Instituição / Organização
2022/07/09 - 2022/07/14 IUBMB-FEBS-PABMB Biochemistry Congress (2022 - 2022)
Congresso (Membro da Comissão Organizadora)
2021/10/14 - 2021/10/16 XXI SPB – National Congress of Biochemistry (2021 - 2021)
Congresso (Membro da Comissão Científica)
Universidade de Évora, Portugal
2021/06/14 - 2021/06/16 7th International Iberian Biophysics Congress (2021 - 2021)
Congresso (Membro da Comissão Organizadora)
2019/03 - 2019/04 12th International Conference on Hydrogenases, Lisbon, Portugal (2019/03/31 - 2019/04/04)
Conferência (Membro da Comissão Organizadora)
2018/06 - 2018/06 6th International Iberian Biophysics Congress and X Iberoamerican Congress of Biophysics, Castellón, Spain (2018/06/20 - 2018/06/22)
Congresso (Membro da Comissão Científica)
2017/07 - 2017/07 XXV National Meeting of the Portuguese Chemical Society, Lisboa, Portugal (2017/07/16 - 2017/07/19)
Encontro (Membro da Comissão Organizadora)
Sociedade Portuguesa de Química, Portugal
2017/07 - 2017/07 19th IUPAB congress and 11th EBSA congress, Edinburgh, Scotland (2017/07/16 - 2017/07/20)
Congresso (Membro da Comissão Científica)
2016/12 - 2016/12 XIX National Congress of Biochemistry, Guimarães, Portugal (2016/12/08 - 2016/12/10)
Congresso (Membro da Comissão Científica)
2016/06 - 2016/06 5th Iberian Biophysics Congress EBSA, Porto, Portugal (2016/06/15 - 2016/06/17)
Congresso (Membro da Comissão Organizadora)
2013/07 - 2013/07 9th European Biophysics Congress EBSA (European Biophysical Societies Association), Lisbon, Portugal (2013/07/13 - 2013/07/17)
Congresso (Membro da Comissão Organizadora)
2012/01 - 2012/01 Jornadas de Bioinformática 2012, Barcelona, Spain (2012/01/23 - 2012/01/25)
Outro (Membro da Comissão Científica)
2011/11 - 2011/11 10th Short course of the Portuguese Biophysical Society "Nanosciences for Life", Santarém, Portugal (2011/11/17 - 2011/11/19)
Outro (Outra)
Sociedade Portuguesa de Biofísica, Portugal
2010/12 - 2010/12 Congresso Nacional de Bioquímica 2010, Porto, Portugal (2010/12/15 - 2010/12/17)
Congresso (Membro da Comissão Científica)
2010/10 - 2010/10 Xth Spanish Symposium on Bioinformatics (JBI2010), Malaga, Spain (2010/10/27 - 2010/10/29)
Simpósio (Membro da Comissão Científica)
2010/10 - 2010/10 9th Short course of the Portuguese Biophysical Society "Protein folding, misfolding and disease", Santarém, Portugal (2010/10/08 - 2010/10/10)
Outro (Membro da Comissão Organizadora)
Sociedade Portuguesa de Biofísica, Portugal
2010/07 - 2010/07 IV Spanish-Portuguese Biophysical Congress, Zaragoza, Spain (2010/07/07 - 2010/07/10)
Congresso (Membro da Comissão Científica)
2009/10 - 2009/11 8th Short course of the Portuguese Biophysical Society "Systems Biology", Santarém, Portugal (2009/10/30 - 2009/11/01)
Outro (Membro da Comissão Organizadora)
Sociedade Portuguesa de Biofísica, Portugal
2008/09 - 2008/09 Workshop “Structure, dynamics, and function of proteins”, Oeiras, Portugal (2008/09/17 - 2008/09/19)
Oficina (workshop) (Membro da Comissão Organizadora)
2008/07 - 2008/07 1st Portuguese-Spanish-British Joint Biophysics Congress 2008, Lisbon, Portugal (2008/07/10 - 2008/07/13)
Congresso (Presidente da Comissão Organizadora)
2007/10 - 2007/10 7th Short course of the Portuguese Biophysical Society "Biospectroscopy and Imaging", Santarém, Portugal (2007/10/19 - 2007/10/21)
Outro (Membro da Comissão Organizadora)
Sociedade Portuguesa de Biofísica, Portugal
2006/09 - 2006/09 Oxizymes in Oeiras: 3rd European Meeting in Oxizymes, Oeiras, Portugal (2006/09/07 - 2006/09/09)
Encontro (Membro da Comissão Organizadora)
2006/09 - 2006/09 VI Ibero-American Congress of Biophysics, Madrid, Spain (2006/09/24 - 2006/09/27)
Congresso (Membro da Comissão Organizadora)
2006/07 - 2006/07 8th European Biological Chemistry Conference, EUROBIC 8, Aveiro, Portugal (2006/07/02 - 2006/07/06)
Conferência (Membro da Comissão Organizadora)
2005/10 - 2005/10 6th Short course of the Portuguese Biophysical Society "From cellular transport to neurosciences: a biophysical perspective", Santarém, Portugal (2005/10/14 - 2005/10/16)
Outro (Membro da Comissão Organizadora)
Sociedade Portuguesa de Biofísica, Portugal
2004/10 - 2004/11 3rd Portuguese-Spanish Biophysics Congress, Lisbon, Portugal (2004/10/29 - 2004/11/01)
Congresso (Presidente da Comissão Organizadora)
2003/10 - 2003/10 5th Short course of the Portuguese Biophysical Society "Genomics and Proteomics: biophysical perspectives", Santarém, Portugal (2003/10/17 - 2003/10/19)
Outro (Membro da Comissão Organizadora)
Sociedade Portuguesa de Biofísica, Portugal
2002/10 - 2002/10 4th Short course of the Portuguese Biophysical Society "Bioenergetics: the cellular power plants", Santarém, Portugal (2002/10/05 - 2002/10/06)
Outro
Sociedade Portuguesa de Biofísica, Portugal
2001/10 - 2001/10 3rd Short course of the Portuguese Biophysical Society "Proteins: from structure to dynamics", Santarém, Portugal (2001/10/04 - 2001/10/06)
Outro (Membro da Comissão Organizadora)
Sociedade Portuguesa de Biofísica, Portugal
1999/10 - 1999/10 2nd Short course of the Portuguese Biophysical Society "Simulation of biological processes. Practical approaches, Santarém, Portugal (1999/10/02 - 1999/10/03)
Outro (Presidente da Comissão Organizadora)
Sociedade Portuguesa de Biofísica, Portugal

Júri de grau académico

Tema
Tipo de participação
Nome do candidato (Tipo de grau)
Instituição / Organização
2021/07 Computational Studies Addressed to PLP-Dependent Enzymes
Arguente principal
Henrique Silva Fernandes (Doutoramento)
Universidade do Porto, Portugal
2021/06 Studies on the function and substrate permeation in ABC transporters by biomolecular simulations
Orientador
Bárbara Abreu (Doutoramento)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2019/07 Computational approaches to virtual screening in human central nervous system therapeutic targets
Arguente principal
Samina Kausar (Doutoramento)
Universidade de Lisboa Faculdade de Ciências, Portugal
2018/03 Anion transmembrane transport by synthetic molecules: a molecular modelling investigation
Arguente principal
Igor Oliveira Marques (Doutoramento)
Universidade de Aveiro, Portugal
2017/12 Computational design and experimental characterization of metallopeptides as proteases for bioengineering applications
Arguente principal
Henrique Daniel Figueiredo Carvalho (Doutoramento)
Universidade de Lisboa Faculdade de Ciências, Portugal
2015/12 Optimization of a MM-PBSA/GBSA protocol for the prediction of binding free energy of Bcl-xL inhibitors
Arguente principal
João Pedro do Vale Hipólito Cavalheiro (Mestrado)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2015/12 Molecular modelling and simulation of pH effects in lipid bilayers
Arguente principal
Diogo Ruivo dos Santos Vila Viçosa (Doutoramento)
Universidade de Lisboa Faculdade de Ciências, Portugal
2014/12 Following amphiphilic molecules on their way through lipid membranes: development of a kinetic model of passive permeation through the blood-brain barrier
Arguente principal
Hugo Alexandre Louro Filipe (Doutoramento)
Hospitais da Universidade de Coimbra, Portugal
2013/09 Constant-pH MD simulations of higher complexity lipid bilayer models: PA/PC binary mixtures
Arguente principal
Hugo Alexandre Feiteira dos Santos (Mestrado)
Universidade de Lisboa Faculdade de Ciências, Portugal
2012/12 Virtual screening with sense and sensibility in the search of new amyloid inhibitors
Arguente principal
Carlos J. V. Simões (Doutoramento)
2012/07 Reductive scavenging of reactive oxygen species in prokaryotes
Arguente
Ana Filipa Pinto (Doutoramento)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2012/03 Propriedades electrónicas de espécies hidrofóbicas micro-solvatadas e em solução
Arguente
Maria Margarida Pires dos Santos Mateus (Doutoramento)
Universidade de Lisboa Faculdade de Ciências, Portugal
2011/01 Characterization of the activity of nitrous oxide reductase: biochemical, spectroscopic and mimetic approaches
Arguente principal
Simone Dell’Acqua (Doutoramento)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2010/11 Molecular modelling of ABC transporter: from ATP hydrolysis to substrate transport
Arguente
Ana Sofia Oliveira (Doutoramento)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2010/11 Protein conformational plasticity and aggregation. Transthyretin and gama-toxin as two case studies
Arguente principal
Nuno Ricardo Santos Loureiro da Silva Ferreira (Doutoramento)
Universidade de Coimbra, Portugal
2010/11 Search based methods for protein structure prediction
Arguente principal
Miguel Mourão Fialho Bugalho (Doutoramento)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2010/09 Dengue virus infection and assembly. A biophysical study for unravelling the role of the capsid protein
Arguente principal
João Miguel Calado da Silva Freire (Mestrado)
Universidade de Lisboa Faculdade de Ciências, Portugal
2010/06 Theoretical study of the reactivity and energetics of organic radicals
Arguente
Filipe Miguel Peres Agapito (Doutoramento)
Universidade de Lisboa Faculdade de Ciências, Portugal
2010/04 CotA-laccase from Bacillus subtilis: structure-function studies of catalytic copper centers
Arguente
Paulo Jorge Rêgo Durão (Doutoramento)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2010/01 Modelação molecular de associações entre aniões e receptors sintéticos
Arguente principal
Sérgio Miguel Fernandes dos Santos (Doutoramento)
Universidade de Aveiro, Portugal
2009/12 Study of the effect of pH on the structure and function of peptides and proteins using molecular simulation methods
Arguente
Sara Isabel Rodrigues Rasteiro de Campos (Doutoramento)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2009/01 Aromatase inhibitors in breast cancer. The discovery of new compounds by computational design and biochemical evaluation
Arguente principal
Marco André Coelho das Neves (Doutoramento)
Universidade de Coimbra, Portugal
2008/12 Ligações de hidrogénio: estudo de alguns aspectos energéticos, electrónicos e dinâmicos por primeiros princípios
Arguente
Sílvia da Conceição Gomes Estácio (Doutoramento)
Universidade de Lisboa Faculdade de Ciências, Portugal
2008/05 Study of CFTR mutants and their processing properties: structural implications
Arguente
Luísa Maria da Silva Pissarra (Doutoramento)
Universidade de Lisboa Faculdade de Ciências, Portugal
2007/10 Superoxide defence strategies in anaerobic prokariotes: The mechanism of superoxide reductases
Arguente
João Vieira Rodrigues (Doutoramento)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2007/10 Structure to function studies in hybrid cluster proteins and glucose-1-phosphate urydylyltranferases
Presidente do júri
David Guerra Aragão (Doutoramento)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2007/10 Enzyme structure and function in nonaqueous solvents
Arguente
Nuno Miguel da Silva Micâelo (Doutoramento)
2007/10 Molecular modelling of redox proteins involved in the oxygen and nitric oxide metabolism
Arguente
Bruno Lourenço da Silva Victor (Doutoramento)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2007/05 Regulation of arabinose metabolism in Bacillus subtilis. Linking structure and function
Arguente
Irina Saraiva Franco (Doutoramento)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2007/03 A non-assigned herpesvirus gene inducing cell cycle arrest and apoptosis
Presidente do júri
Rute Nascimento (Doutoramento)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2007/03 Hydrogen metabolism in Desulfovibrio vulgaris Hildenborough
Arguente
Ana Filipa de Matos Almeida Valente (Doutoramento)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2007/02 The Role of Flavodiiron Proteins in Nitric Oxide Detoxification
Arguente
João Filipe Bogalho Vicente (Doutoramento)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2007/02 Molecular modelling of redox proteins involved in the hydrogen metabolism
Arguente
Vitor Hugo Oliveira Teixeira (Doutoramento)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2006/12 Thermodynamic and kinetic characterisation of multiheme cytochromes
Arguente
Catarina Morais Vaz Paquete (Doutoramento)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2005/12 Assembly of the Bacillus subtilis spore coat
Arguente
Teresa Vasconcelos Costa (Doutoramento)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2005/10 Structural and functional studies on the human salvage enzyme thymidine kinase 2
Arguente principal
João Filipe Viegas Barroso (Doutoramento)
Universidade de Coimbra, Portugal
2004/06 Study of the localization of fucosyltransferase III. Importance of the transmembrane and cytosolic domains
Arguente
Vitor Lino Sousa (Doutoramento)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2003/12 Integrating protein structural information
Arguente principal
Ludwig Krippahl (Doutoramento)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2003/10 The crystal structure of cytochrome c nitrite reductase from Desulfovibrio desulfuricans and modelling studies of electron transfer between flavodoxin and mono-heme cytochromes
Arguente
Carlos Manuel Alves da Costa Cunha (Doutoramento)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2003/07 Structural studies of the tetrahaem cytochrome c3 and nine haem cytochrome c from Desulfovibrio desulfuricans ATCC 27774 in the oxidised and reduced state. Correlation with cooperativity effects
Arguente
Isabel Maria Travassos de Almeida de Jesus Bento (Doutoramento)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2002/10 Protein stabilisation by diglycerol phosphate, a compatible solute from hyperthermophiles
Arguente
Pedro Miguel Lamosa (Doutoramento)
2001/11 Simulação de interacções intermoleculares em sistemas de interesse farmacológico
Arguente principal
Elsa Fernanda de Sousa Henriques (Doutoramento)
Universidade do Porto Faculdade de Ciências, Portugal
2001/05 Estudos de modelação e de ressonância magnética nuclear de complexos de inclusão entre ciclodextrinas e poliazamacrocíclos de gadolínio (III)
Arguente principal
Carla Sofia de Oliveira Ferreira (Mestrado)
Universidade do Porto Faculdade de Ciências, Portugal
2000/07 A determinação de propriedades estruturais, conformacionais e dinâmicas de moléculas em sistemas modelo de membranas e em solução
Arguente principal
Miguel Xavier Jesus Josefat Fernandes (Doutoramento)
Universidade de Lisboa Faculdade de Ciências, Portugal
2000/07 Modelling sidechain conformation in proteins
Orientador
Joaquim Pires Antunes Mendes (Doutoramento)

Curso / Disciplina lecionado

Disciplina Curso (Tipo) Instituição / Organização
2022 - 2022 Biomolecular Simulation Computational Biology and Bioinformatics (Mestrado) Universidade Nova de Lisboa, Portugal
2014 - 2022 Co-responsible of the course Advanced Topics in Bioinformatics Bioquímica para a Saúde (Mestrado) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2014 - 2022 Responsible for the Protein biogenesis, folding and structure curricular unit Biociências Moleculares (Doutoramento) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2021 - 2021 Fundamentals of Computational Biology Computational Biology and Bioinformatics (Mestrado) Universidade Nova de Lisboa, Portugal
2021 - 2021 Perspectives in Computational Biology Computational Biology and Bioinformatics (Mestrado) Universidade Nova de Lisboa, Portugal
2018/05/21 - 2018/05/24 Biomolecular modelling / Structural Bioinformatics Bioquimica Médica (Doutoramento) Universidade Federal do Rio de Janeiro, Brasil
2007 - 2018 Molecular modelling methodologies MIT-Portugal Bioengineering PhD program (Doutoramento)
2017/05 - 2017/05 Biomolecular modelling PhD Course in Pharmaceutical Biophysics Universidade de Lisboa Faculdade de Farmácia, Portugal
2009 - 2017 Biomolecular modelling techniques Engenharia Biológica (Mestrado integrado) Universidade de Lisboa Instituto Superior Técnico, Portugal
2015 - 2016 Molecular modelling methodologies Bionanotecnologia (Mestrado) Universidade de Lisboa Instituto Superior Técnico, Portugal
2014/05/12 - 2014/05/16 Biomolecular modelling / Structural Bioinformatics Bioquimica Médica (Doutoramento) Universidade Federal do Rio de Janeiro, Brasil
2014 - 2014 Molecular mechanics/dynamics, Molecular Visualization and Protein Structure Prediction Ciências Biomédicas (Mestrado integrado) Universidade do Algarve, Portugal
2013 - 2014 Molecular modelling methodologies Gulbenkian Programme In Integrative Biomedical Sciences (Doutoramento)
1999 - 2013 Molecular modelling methodologies ITQB PhD Program (Doutoramento) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2012 - 2012 Biomolecular modelling applications Bioinformática (Mestrado) Universidade de Lisboa Faculdade de Ciências, Portugal
2005 - 2010 Biomolecular modelling techniques Química Inorgânica Biomédica: Aplicações em Diagnóstico e Terapia (Mestrado) Universidade de Lisboa Faculdade de Ciências, Portugal
2009 - 2009 Biomolecular modelling techniques Genética Molecular e Biomedicina (Mestrado integrado) Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2005 - 2009 Molecular modelling methodologies Gulbenkian Program in Computational Biology (Doutoramento)
2008 - 2008 An overview of Biomolecular modelling techniques in the course of Perspectives in Biochemistry Bioquímica (Licenciatura) Universidade do Minho, Portugal
2007 - 2007 Protein structure prediction methodologies Bioinformática (Mestrado integrado) Universidade do Minho, Portugal
2006 - 2006 Biomolecular modelling in the course of Molecular modeling Química (Licenciatura) Universidade do Minho, Portugal
2005 - 2005 An overview of Biomolecular modelling techniques in the course of Perspectives in Chemistry and Biochemistry Química (Licenciatura) Universidade de Lisboa Faculdade de Ciências, Portugal
1998 - 2005 Molecular modelling techniques in the course of Molecular Biophysics Bioquímica (Licenciatura) Universidade de Lisboa Faculdade de Ciências, Portugal
2004 - 2004 Protein structure prediction in the course of Bioinformatics Engenharia Biomédica (Licenciatura) Universidade do Minho, Portugal
2004 - 2004 Biomolecular modelling techniques Química Farmacêutica (Mestrado) Universidade de Lisboa Faculdade de Farmácia, Portugal
2003 - 2003 Molecular modelling techniques Genética Molecular (Mestrado integrado) Universidade do Minho, Portugal
2002 - 2002 Molecular modelling techniques in the course of Simulation Ciências da Engenharia - Engenharia Biomédica e Biofísica (Licenciatura) Universidade de Lisboa Faculdade de Ciências, Portugal
2002 - 2002 Molecular modelling techniques Biofísica (Mestrado) Universidade de Lisboa Faculdade de Ciências, Portugal
2002 - 2002 Molecular modelling techniques in the course of Bioinformatics Biotecnologia (Mestrado) Universidade do Algarve, Portugal
1997 - 2001 Molecular modelling biologia e medicina (Doutoramento) Instituto Gulbenkian de Ciência, Portugal

Membro de associação

Nome da associação Tipo de participação
1994 - Atual Portuguese Biochemical Society
1994 - Atual Portuguese Biophysical Society
1994 - Atual Portuguese Chemical Society
1994 - Atual The Biophysical Society (USA)

Membro de comissão

Descrição da atividade
Tipo de participação
Instituição / Organização
2019/10 - 2019/10 Member of the selection committee for the selection of a Researcher with a Doctorate – “Abertura de Procedimento Concursal de Seleção Internacional para a Contratação de Investigador(a) Júnior
Membro
Universidade de Lisboa Faculdade de Farmácia, Portugal
2018/12 - 2018/12 Member of the selection committee for the selection of a Researcher with a Doctorate – “Procedimento concursal para recrutamento de um investigador, para o exercício de atividades de investigação científica
Membro
Universidade de Évora, Portugal
2018/06 - 2018/06 Member of the selection committee for a “Chefe de Divisão” position in the Divisão de Apoio a Bolsas from “Fundação para a Ciência e Tecnologia”
Membro
Fundação para a Ciência e a Tecnologia, Portugal
2016/06 - 2016/07 Member of the selection committee for four Assistant Researcher positions within the Research Unit MOSTMICRO from ITQB NOVA
Membro
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Molecular, Structural and Cellular Microbiology – MOSTMICRO Research Unit of ITQB NOVA, Portugal
2015/11 - 2015/11 Member of the selection committee for one Assistant Professor position in the Faculty of Medicine from Lisbon University
Membro
Universidade de Lisboa Faculdade de Medicina, Portugal
2012/04 - 2012/04 Member of the selection committee for one Research position (Investigador Principal) of the Associated Laboratory ITQB/IGC/IBET/CEDOC
Membro
2008/12 - 2008/12 Member of the selection committee for a Research position (Investigador Auxiliar) of FFUC
Membro
Universidade de Coimbra Faculdade de Farmácia, Portugal
2008/10 - 2008/10 Member of the selection committee for a Research position (Investigador Auxiliar) of FCUL
Membro
Universidade de Lisboa Faculdade de Farmácia, Portugal
2007/09 - 2007/10 Member of the selection committee for a Research position (Investigador Auxiliar) of FFUL
Membro
Universidade de Lisboa Faculdade de Farmácia, Portugal
2007/09 - 2007/09 Member of the selection committee for 18 Research positions (Investigador Auxiliar) of ITQB-UNL/IBET
Membro
2006/06 - 2006/06 Member of the selection committee for a Research position (Investigador Auxiliar) of ITQB-UNL
Membro
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2005/11 - 2005/11 Member of the selection committee for a Research position (Investigador Auxiliar) of ITQB-UNL
Membro
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2005/06 - 2005/06 Member of the selection committee for two Research positions of the Associated Laboratory ITQB/IGC/IBET
Membro
2003/10 - 2003/10 Member of the selection committee for four Research positions of the Associated Laboratory ITQB/IGC/IBET
Membro
2003/09 - 2003/09 Member of the selection committee for the Research position in Protein Crystallography of the Associated Laboratory REQUIMTE (FCT-UNL, Portugal)
Membro
REQUIMTE Unidade de Ciências Biomoleculares Aplicadas, Portugal

Outro júri / avaliação

Descrição da atividade Instituição / Organização
2018 - Atual Member the Editorial Board of the FEBS Open Bio Journal
2013 - Atual Member the Editorial Board of the Scientific Reports Journal
2012 - Atual Member the Editorial Board of the PLOS One Journal
2019 - 2022 Member (2019) and Vice-Chair (2020 and 2021) of the EX4 (Human biology and medical sciences) discipline panel for evalution of EXPRO Grants. Czech Science Foundation Akademie ved Ceske republiky, República Checa
2020 - 2021 Member of the International Review Panel evaluating research proposals for the National Science Centre National Science Centre, Polónia
2017 - 2019 Evaluator of Second Triennium Pos-doctoral Fellowship proposals Fundação para a Ciência e a Tecnologia, I.P., Portugal
2011 - 2019 Member of the Editorial Board of the Biophysical Reviews Journal
2018 - 2018 Evaluator of proposals for the Innovate Competition of the IMed Conference
2016 - 2018 Chair of the Experimental Biology and Biochemistry panel for the national evaluation of PhD and Post-Doctoral Fellowships Fundação para a Ciência e a Tecnologia, I.P., Portugal
2017 - 2017 Evaluation of two projects from the National Science Centre Narodowe Centrum Nauki, Polónia
2017 - 2017 Evaluation of one project from the Deutsche Forschungsgemeinschaft (German Research Foundation) on the Emmy Noether Programme Deutsche Forschungsgemeinschaft, Alemanha
2017 - 2017 Evaluation one individual proposal (36 months) from the Deutsche Forschungsgemeinschaft (German Research Foundation) Deutsche Forschungsgemeinschaft, Alemanha
2016 - 2016 Evaluation of one project from the United States-Israel Binational Science Foundation Binational Science Foundation, Israel
2016 - 2016 Evaluation of one project from the National Science Centre Narodowe Centrum Nauki, Polónia
2015/11 - 2015/11 Evaluation of Marie Curie fellowships - H2020-MSCA-IF-2015 call
2013/10 - 2013/10 Evaluation of Marie Curie fellowships - FP7-PEOPLE-2013-IEF-IIF-IOF LIF call
2013/07 - 2013/07 Evaluation of FP7 ERA Chairs
2013/01 - 2013/02 Member of the jury of the Santander Totta – Universidade Nova de Lisboa award, 2012/2013 Edition
2013 - 2013 Evaluation of one project from the National Science Centre Narodowe Centrum Nauki, Polónia
2013 - 2013 Evaluation of one project for the Austrian Science Fund Fonds zur Förderung der wissenschaftlichen Forschung, Áustria
2012/10 - 2012/10 Evaluation of Marie Curie fellowships - FP7-PEOPLE-2012-IEF-IIF-IOF LIF call
2012/08 - 2012/08 Evaluation of a project from the Romanian National Research Council
2012/07 - 2012/07 Evaluation of National Fundação para a Ciência e Tecnologia PhD and Post-Doctoral fellowships - Biological Sciences Panel Fundação para a Ciência e a Tecnologia, I.P., Portugal
2012/07 - 2012/07 Evaluation of a project from the American Chemical Society Petroleum Research Fund American Chemical Society, Estados Unidos
2012/04 - 2012/04 Evaluation of Marie Curie Career Integration Grants - FP7-PEOPLE-2012-CIG call
2012 - 2012 Evaluation of two projects from the National Science Center, Poland
2011/10 - 2011/10 Evaluation of Marie Curie fellowships - FP7-PEOPLE-2011-IEF-IIF-IOF LIF call
2011/04 - 2011/04 Evaluation of Marie Curie Career Integration Grants - FP7-PEOPLE-2011-CIG call
2011 - 2011 Evaluation of a project from the National Science Foundation National Science Foundation, Estados Unidos
2011 - 2011 Evaluation of a project from the Emmy Noether-Programm Nachwuchsgrupper Neuantrag Deutsche Forschungsgemeinschaft, Alemanha
2011 - 2011 Evaluation of two projects for the Austrian Science Fund Fonds zur Förderung der wissenschaftlichen Forschung, Áustria
2011 - 2011 Evaluation of two research projects for the Cyprus Research Promotion Foundation Cyprus Research Promotion Foundation, Chipre
2011 - 2011 Evaluation of a research proposal from Agência de Inovação Agência Nacional de Inovação SA, Portugal
2007 - 2011 Evaluation of projects PICT Agencia Nacional De Promoción Científica Y Tecnológica, Argentina
2010/10 - 2010/10 Evaluation of Marie Curie fellowships - FP7-PEOPLE-2010-IEF-IIF-IOF LIF call
2009/10 - 2009/10 Evaluation of Marie Curie fellowships - FP7-PEOPLE-2009-IEF-IIF-IOF LIF call
2009 - 2009 Evaluation of a project from the NWO Grant Agency of The Netherlands Nederlandse Organisatie voor Wetenschappelijk Onderzoek, Países Baixos
2008/10 - 2008/10 Evaluation of Marie Curie fellowships - FP7-PEOPLE-IEF/IOF/IIF-2008 LIF call
2008 - 2008 Evaluation of a project from the Grant Agency Akademie ved Ceske republiky, República Checa
2006/04 - 2006/05 Evaluation of Marie Curie fellowships - FP6-Mobility-5/6/7 LIF call
2005/02 - 2005/03 Evaluation of Marie Curie Research Training Networks - FP6-2004-Mobility-1 call
2004/05 - 2004/05 Evaluation of FP6-NEST research projects
2004/02 - 2004/03 Evaluation of Marie Curie Research Training Networks - FP6-2002-Mobility-1 call
Distinções

Outra distinção

2023 Oeiras Municipal Medal of Merit, Gold Grade (Medalha Municipal de Mérito, grau ouro)
Camara Municipal Oeiras, Portugal