Claudio Manuel Simões Loureiro Nunes Soares (DE12-5674-E511)

Curriculum Vitae

Claudio Manuel Simões Loureiro Nunes Soares

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.

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Identification

Personal identification

Full name: Claudio Manuel Simões Loureiro Nunes Soares

Citation names

Soares, Claudio M.

Author identifiers

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

Email addresses

claudio@itqb.unl.pt (Professional)

Telephones

Telephone

214469734 (Professional)

Addresses

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 (Professional)

Websites

http://www.itqb.unl.pt/~claudio (Professional)
http://www.itqb.unl.pt/pm (Scholar)

Knowledge fields

Natural sciences - Biological Sciences - Biochemistry
Natural sciences - Biological Sciences - Biophysics
Exact Sciences - Computer and Information Sciences - Bioinformatics

Languages

Language	Speaking	Reading	Writing	Listening
Portuguese	Advanced (C1)	Advanced (C1)	Advanced (C1)	Advanced (C1)
English	Advanced (C1)	Advanced (C1)	Advanced (C1)	Advanced (C1)
Spanish; Castilian	Intermediate (B1)	Intermediate (B1)	Beginner (A1)	Intermediate (B1)
Swedish	Beginner (A1)	Beginner (A1)	Beginner (A1)	Beginner (A1)
French	Beginner (A1)	Intermediate (B1)	Beginner (A1)	Beginner (A1)

Education

	Degree	Classification
2021/05/25 - 2021/05/25 Concluded	Biociências Moleculares (Título de Agregado) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
1990/11/01 - 1994/10/03 Concluded	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" (THESIS/DISSERTATION)	With honours
1994 Concluded	Filosofie Licentiatexamen (a Swedish degree higher than Master) (Outros) Uppsala Universitet, Sweden	Without classification
1986/09/01 - 1989/09/30 Concluded	Bioquímica (Licenciatura) Universidade de Lisboa Faculdade de Ciências, Portugal "Estudos sobre aldeído desidrogenases de fígado de rato" (THESIS/DISSERTATION)	17 (in a scale of 20)

Affiliation

Teaching in Higher Education

	Category Host institution	Employer
2022/04/01 - Current	Full Professor (University Teacher)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

2005/03/01 - 2022/03/31	Associate Professor (University Teacher)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

1999/02/01 - 2005/02/28	Invited Assistant Professor (University Teacher)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Positions / Appointments

	Category Host institution	Employer
2020/06/01 - Current	President of the Scientific Council	TAGUSPARK – Parque de Ciência e Tecnologia, Portugal

2016/10/01 - Current	Member of European Science Foundation (ESF) College of Expert Reviewers	European Science Foundation, France

2023/05/01 - 2025/10/06	Pro-Rector	Universidade Nova de Lisboa, Portugal
	Universidade Nova de Lisboa, Portugal
2013/03 - 2023/04/30	President of the Scientific Council	Universidade Nova de Lisboa, Portugal
	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2013/03 - 2023/04/30	President of the Pedagogic Council	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

Others

	Category Host institution	Employer
2015/01/01 - Current	Coordinator	Molecular, Structural and Cellular Microbiology – MOSTMICRO Research Unit of ITQB NOVA, Portugal

2008/11/01 - Current	First Secretary of the General Assembly	Sociedade Portuguesa de Biofísica, Portugal

1999/02/01 - Current	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, United Kingdom

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, United Kingdom

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, Sweden

1988/10/01 - 1989/09/30	Diploma student	Universidade de Lisboa Faculdade de Ciências, Portugal

Projects

Grant

	Designation	Funders
2024/01/01 - Current	Small biologics discovery: unlocking new antivirals for pandemic preparedness - ID 2023.00583.BD 2023.00583.BD École Polytechnique Fédérale de Lausanne, Switzerland Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica António Xavier, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2025/01 - 2029/12	MOLECULAR STRATEGIES AGAINST VIRAL ENTRY AND GLYCAN SHIELDING 101191794	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 Provided by PTCRIS: 141512	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 Principal investigator	Partnership for Advanced Computing In Europe Ongoing
2013/03 - 2015/03	Structural Determinants of Oxygen Tolerance in a NiFeSe Hydrogenase 125671 Provided by PTCRIS: 125671	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 Provided by PTCRIS: 83705 83705	Fundação para a Ciência e a Tecnologia, I.P.
2007/01 - 2008/12	Rationalization of cutinase enantioselectivity in nonaqueous media Provided by PTCRIS: 82386 82386	Fundação para a Ciência e a Tecnologia, I.P.

Contract

	Designation	Funders
2023/09/01 - Current	Life Sciences for a Healthy and Sustainable Future LA/P/0087/2020 10.54499/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 Ongoing
2021/01/01 - Current	PI3K / AKT / mTOR pathway modulation as target therapy in the treatment of breast and colorectal cancer 2019.00199.CBM Principal investigator Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2020/12/01 - Current	Design of protein chimeras targeting SARS-CoV-2 FCT/CPCA/A0/7305/2020 Researcher Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2020/12 - Current	Design of protein chimeras targeting SARS-CoV-2 FCT/CPCA/A0/7305/2020	Fundação para a Ciência e a Tecnologia
2020/07/01 - Current	A practical assay for routine detection of neutralizing antibodies against SARSCoV2 that bypasses requirements for high biosafety laboratory usage 613719605 Researcher Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2020/06/01 - Current	Predicting SARS-CoV-2 susceptibility by tracking the genetic variability of the ACE2 receptor 613747728 Researcher Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
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 Ongoing
2019/01 - 2022/12	Using computational and experimental methods to provide a global characterization of viral fusion peptides PTDC/CCI-BIO/28200/2017 Principal investigator	Fundação para a Ciência e a Tecnologia Ongoing
2019 - 2022	SHIKIFACTORY100 - Modular cell factories for the production of 100 compounds from the shikimate pathway H2020-NMBP-BIO-2018 Principal investigator	Ongoing
2016/01 - 2018/12	Engineering a highly active NiFeSe Hydrogenase for electrocatalytic and photocatalytic applications PTDC/BBB-BEP/2885/2014 Principal investigator	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 Principal investigator	Partnership for Advanced Computing In Europe
2015/01 - 2017/12	Molecular, Structural and Cellular Microbiology Provided by PTCRIS: 147361	Fundação para a Ciência e a Tecnologia
2014/01 - 2015/12	Incentive - LA 4 - 2014 Provided by PTCRIS: 137336	Fundação para a Ciência e a Tecnologia
2013/03 - 2014	Structural Determinants of Oxygen Tolerance in a NiFeSe Hydrogenase PTDC/BBB-BEP/0934/2012 Principal investigator	Fundação para a Ciência e a Tecnologia, I.P. Concluded
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 Principal investigator	Concluded
2010 - 2014	Membrane fusion mechanism of Influenza Hemagglutinin: a simulation and biophysical approach. 114774 Provided by PTCRIS: 114774 Principal investigator	Fundação para a Ciência e a Tecnologia, I.P. Concluded
2010 - 2014	Proton transfer and proton pumping in haem-copper oxidases. Methodological developments and their application to unravel the molecular mechanism. Provided by PTCRIS: 113446 113446 Principal investigator	Fundação para a Ciência e a Tecnologia, I.P. Concluded
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 Concluded
2010/01 - 2012/12	Breaking Down The Wall - Microbial Hemicellulases for saccharification 102345 Provided by PTCRIS: 102345 Principal investigator	Fundação para a Ciência e a Tecnologia, I.P. Concluded
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 Principal investigator	Fundação para a Ciência e a Tecnologia, I.P. Concluded
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 Concluded
2010/01 - 2012	Study of pH-dependent protein misfolding using state-of-the-art molecular modeling methods Provided by PTCRIS: 105238 105238 Researcher	Fundação para a Ciência e a Tecnologia, I.P. Concluded
2010/01 - 2012	Including protonation effects in the simulation of peptides and proteins in membrane environments Provided by PTCRIS: 104378 104378 Researcher	Fundação para a Ciência e a Tecnologia, I.P. Concluded
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 Provided by PTCRIS: 73946 73946 Principal investigator	Fundação para a Ciência e a Tecnologia, I.P. Concluded
2009/01 - 2011/12	Investigation of redox-state-specific protein-protein interactions and energy transduction in the electron transfer chains of sulfate reducing bacteria 65640 Provided by PTCRIS: 65640 Principal investigator	Fundação para a Ciência e a Tecnologia, I.P. Concluded
2008 - 2010	Microbial enzymes involved in superoxide and nitric oxide reduction 67263 Provided by PTCRIS: 67263 Principal investigator	Fundação para a Ciência e a Tecnologia, I.P. Concluded
2007 - 2010	Towards biohydrogen production - study of a high-activity, oxygen-resistant bacterial hydrogenase Provided by PTCRIS: 70429 70429 Principal investigator	Fundação para a Ciência e a Tecnologia, I.P. Concluded
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 Principal investigator	Concluded
2007/01 - 2008/11	Heme-copper oxygen reductases - mechanisms of electron/proton transfer and oxygen reduction 82169 Provided by PTCRIS: 82169 Provided by PTCRIS: 58608 58608	Fundação para a Ciência e a Tecnologia, I.P.
2005 - 2008	Rationalization of cutinase enantioselectivity in nonaqueous media Provided by PTCRIS: 57193 57193 Principal investigator	Fundação para a Ciência e a Tecnologia, I.P. Concluded
2005 - 2008	Nano-Engineering of Bacterial Laccases Provided by PTCRIS: 57083 57083 82550 Provided by PTCRIS: 82550 Principal investigator	Fundação para a Ciência e a Tecnologia, I.P. Concluded
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 Concluded
2003 - 2006	Increasing realism in protein modelling: including pH and redox effects into molecular dynamics simulations info:eu-repo/grantAgreement/FCT/POCI/45810/PT Researcher	Universidade do Algarve Faculdade de Ciências e Tecnologia Concluded
2002 - 2005	Folding, Processing and Function of Normal and Mutant Cystic Fibrosis Transmembranar Conductance Regulator: Structural Implications info:eu-repo/grantAgreement/FCT/POCI/47382/PT Principal investigator	Universidade do Algarve Faculdade de Ciências e Tecnologia Concluded
2001/07 - 2004/06	Molecular modelling of key redox proteins in bacterial metabolism: methodology and applications 32789 Provided by PTCRIS: 32789 Principal investigator	Fundação para a Ciência e a Tecnologia, I.P. Concluded
2001/01/01 - 2004	Electron transfer mechanisms and dynamics of a proton thruster: cytochrome c3 info:eu-repo/grantAgreement/FCT/POCI/43323/PT Principal investigator	Universidade do Algarve Faculdade de Ciências e Tecnologia Concluded
2001 - 2003	Novel respiratory complexes: Molecular basis for energy transduction POCTI/BME/32789/99 Principal investigator	Universidade do Algarve Faculdade de Ciências e Tecnologia Concluded
2000/10/01 - 2002	Structure-function relationships of serine hydrolases in non-conventional media PRAXIS/P/BIO/14314/1998 Principal investigator	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) Principal investigator	Concluded
1997 - 1998	Structural determinants of electron transfer interactions between [Ni-Fe] hydrogenase and cytochrome c3 from D.desulfuricans ATCC 27774 PRAXIS XXI project Principal investigator	Concluded
1997 - 1998	Structural determination of proteins using X-ray crystallography and its structural implications PRAXIS XXI project Principal investigator	Concluded
1996 - 1998	Construction of novel redox proteins from modular building blocks EC BIOTECNOLOGY PROGRAM AREA 6.1 project (BIO4-CT96-0413) Principal investigator	Concluded
1996 - 1997	Crystal structure determination and molecular modelling of proteases and electron transfer proteins JNICT Luso-Hungariun project Principal investigator	Concluded

Outputs

Publications

Book	Lousa, D.; Baptista, A.M.; Soares, C.M.. Hydration effects on enzyme properties in nonaqueous media analyzed by MD simulations. 2016. 10.4032/9789814669337 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
Book chapter	Bento, I.; Louro, RO; Soares, Claudio M.; Carrondo, MA. "Tetraheme cytochromes c3". In Handbook on Metalloproteins, edited by john wiley, 5-15. CRC Press, 2011. I Bento; Maria Arménia Carrondo; Claudio M. Soares; Ricardo Louro. "Tetraheme cytochromes C". edited by A. Messerschmidt, 5-15. John Wiley & Sons, 2011. Carrondo, M.A.; Soares, Claudio M.; Matias, PM. "Nine-heme cytochrome c". In Handbook on Metalloproteins. CRC Press, 2001.
Conference abstract	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". Paper presented in 3D-Biodata-PT (3rd Annual Meeting), Lisboa, 2024. Accepted 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).". Paper presented in Biophysics Festival – 4th Meeting of Young Biophysicists, Covilhã, 2024. Accepted 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)". Paper presented in Biophysics Festival – 4th Meeting of Young Biophysicists, Covilhã, 2024. Accepted 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". Paper presented in European Biophysical Societies' Association (EBSA) congress 2023, stockholm, 2023. 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". Paper presented in 25thIUBMB-46thFEBS-15thPABMB Congress, Lisbon, 2022. Accepted 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. Published 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 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". Paper presented in 9th International Conference on Nanosciences & Nanotechnologies (NN12), Thessaloniki, 2012. Published
Conference poster	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". Paper presented in Mini-symposium on Computational Biophysics: From Machine Learning to Coarse-Grained Simulations, 2025. 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". Paper presented in NOVAHealth Conference: Tackling Pandemics: Strategies for Prevention, Preparedness and Response, 2024. 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". Paper presented in FEBS3+ Meeting, 2024. 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". Paper presented in European South Athlantic Biophysics Congress, 2024. 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.". Paper presented in European South Atlantic Biophysics Congress, 2024. 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". Paper presented in Biophysics Festival – 4th Meeting of Young Biophysicists, Covilhã, Portugal, 9-10 May, 2024. Correia, João; Ferreira, Sofia; Rocha, Isabel; Lousa, Diana; Souza, Caio S.; Soares, Claudio M.. "A Computational Pipeline To Automate Gene Discovery and Enzyme Engineering". Paper presented in 4rd Meeting of Young Biophysicists "Biophysics Festival 2024", 2024. 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". Paper presented in Bioinformatic Open Days 2024, 2024. 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". Paper presented in Bioinformatics Open Days 2024, 2024. 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". Paper presented in Bioinformatics Open Days 2024, 2024. 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". Paper presented in Bioinformatics Open Days 2024, 2024. 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". Paper presented in NOVAHealth Conference: Tackling Pandemics: Strategies for Prevention, Preparedness and Response, 2024. 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". Paper presented in PEGS Europe: Protein & Antibody Engineering Summit, 2023. 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. 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". Paper presented in EMBO Workshop - Mechanisms of membrane fusion, 2023. 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". Paper presented in BIOPHYSICS FESTIVAL - 3rd Meeting of Young Biophysicists, 2023. 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.. Corresponding author: Moreira, Pedro. "Developing antivirals for the future". Paper presented in 3rd Meeting of Young Biophysicists, 2023. 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". Paper presented in Bioinformatics Open Days 2023, 2023. 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". Paper presented in IUBMB-FEBS-PABMB 2022 The Biochemistry Global Summit, 2022. Parreiras, Susana; Cruz, Carlos H.; Valério, Mariana; Sousa, Pedro M. F.; Soares, Claudio M.; Vicente, João B.; Lousa, Diana. Corresponding author: Parreiras, Susana. "Design, production and characterization of antiviral proteins targeting SARS-CoV-2". Paper presented in The Biochemistry Global Summit Lisbon, 2022. Fernandes, Bárbara C.; Cruz, Carlos H.; Parreiras, Susana; Silva, Elísio; Soares, Claudio M.; Melo, Manuel N.; Lousa, Diana; Vicente, João B.. Corresponding author: Fernandes, Bárbara C.. "Engineered proteins targeting SARS-CoV-2". Paper presented in 2nd Portuguese Young Biophysicists' Meeting, 2022. Teixeira, Rita I.; Valério, Mariana; Borges-Araújo, Luis; Manuel N. Melo; Vicente, João B.; Lousa, Diana; Soares, Claudio M.. Corresponding author: Lousa, Diana. "The impact of SARS-CoV-2 Omicron variant on the human ACE2 binding: a computational study". Paper presented in 2nd Portuguese Young Biophysicists¿ Meeting, Biophysics Festival 2022,, 2022. 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". Paper presented in V International Conference NOVA health Chronic Disease and Infection, 2022. Parreiras, Susana; Cruz, Carlos H.; Valério, Mariana; Sousa, Pedro M. F.; Soares, Claudio M.; Vicente, João B.; Lousa, Diana. Corresponding author: Parreiras, Susana. "Design and production of antiviral proteins targeting SARS-CoV-2". Paper presented in 8th Meeting of Young Researchers in Computational Structural Biology 2021, 2021. 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". Paper presented in VIII Encontro de Jovens Investigadores em Biologia Computacional Estrutural, Coimbra, 2021. 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". Paper presented in VIII Encontro de Jovens Investigadores em Biologia Computacional Estrutural, Coimbra, 2021. Parreiras, Susana; Cruz, Carlos H.; Valério, Mariana; Soares, Claudio M.; Vicente, João B.; Lousa, Diana. Corresponding author: Parreiras, Susana. "Rationally designed antiviral proteins targeting SARS-CoV-2". Paper presented in 10th edition of Bioinformatics Open Days 2021, 2021. 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". Paper presented in 2nd European International Society for Microbial Electrochemistry and Technology Meeting, 2014. 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". Paper presented in IV Bienal of NMR, 2008.
Journal article	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 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 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 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 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 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 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 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 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 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 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 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 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): Accepted 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Lousa, D.; Baptista, A.M.; Soares, C.M.. 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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 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 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". 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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 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 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". 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"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 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 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 Serrano, M.; Neves, A.; Soares, C.M.; Moran Jr., C.P.; Henriques, A.O.. "Role of the anti-sigma factor SpoIIAB in regulation of s^G 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 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 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 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 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 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 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 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 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. 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. 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 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 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 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 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 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 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 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 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 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. 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 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 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 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 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 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 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 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 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 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 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. 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 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. 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 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 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 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 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. 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 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 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

Other

Other output

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
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

Activities

Oral presentation

	Presentation title	Event name Host (Event location)
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, Austria)
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, Spain)
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, Spain)
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, Brazil)
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, Germany)
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, United States)
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, Australia)
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, Australia)
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, France)
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, Belgium)
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, Germany)
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, Brazil)
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, Germany)
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, Germany)
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, United States)
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, Germany)
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, Greece)
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, Italy)
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, Spain)
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, Spain)
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, Italy)
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, Spain)
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, United States)
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, Switzerland)
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, France)
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, Italy)
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, United Kingdom)
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, Spain)

Supervision

	Thesis Title Role	Degree Subject (Type) Institution / Organization
2019/05 - Current	Computational enzyme engineering Supervisor	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2017/09 - Current	Metabolic Engineering aided by computer-guide enzyme engineering for the optimization of cell factories Co-supervisor of Joana Filipa Azevedo Oliveira	Bioengenharia (PhD) Universidade do Minho, Portugal
2017/09 - Current	Viral Membrane Fusion: Structural determinants and dynamical behaviour Supervisor	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2016/01 - Current	The structural basis of substrate translocation in ABC transporters: a biomolecular simulation approach Supervisor	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2016/01 - Current	Efficient algorithms for protein docking Co-supervisor	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal Universidade de Lisboa Instituto Superior Técnico, Portugal
2016/01 - Current	Genome-scale modeling of allosteric regulation in E. coli Co-supervisor	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal Universidade do Minho, Portugal
2014/01 - Current	Membrane altering proteins: a computational study of viral membrane fusion and antimicrobial peptides Supervisor of Davide Ribeiro da Cruz	Bioquímica (PhD) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2013/03 - Current	Molecular mechanisms of viral membrane fusion: A computational analysis Supervisor	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2008/01 - Current	Ligand interaction and binding in laccases – reduced substrates, dioxygen and protons Supervisor	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 Co-supervisor	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 Co-supervisor of Tiago Filipe Coelho Resende	Bioengenharia (PhD) 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 Co-supervisor	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. Supervisor	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2011 - 2016/03	Modelação molecular/bioinformática estrutural da hemaglutinina do vírus influenza Supervisor of Jorge Miguel Penela Deus Antunes	Bioquímica (Master) Universidade de Lisboa Faculdade de Ciências, Portugal
2008 - 2012	Molecular mechanisms of membrane fusion in influenza virus Supervisor	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 Supervisor	Universidade de Lisboa Faculdade de Ciências, Portugal
2006/09 - 2007/10	Modelação molecular dos domínios de ligação de nucleótido de um transportador ABC Supervisor	Universidade de Lisboa Faculdade de Ciências, Portugal
2002/11 - 2007/02	Molecular Modelling of Redox Proteins Involved in the Hydrogen Metabolism Supervisor of Vítor Hugo Oliveira Teixeira	Bioquímica (PhD) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2003/04 - 2007	Enzyme Structure and Function in Nonaqueous Solvents Supervisor of Nuno Miguel da Silva Micaêlo	Bioquímica (PhD) 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 Supervisor of Bruno Lourenço da Silva Victor	Bioquímica (PhD) 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. Supervisor	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2006 - 2006	Molecular Modelling of Abc Transporters: from Atp Hydrolysis to Substrate Transport Supervisor of Ana Sofia Fernandes de Oliveira	Bioquímica (PhD) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2006 - 2006	Molecular determinants of nonaqueous biocatalysis: A computational analysis Supervisor of Diana Andreia Pereira Lousa	Bioquímica (PhD) 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 Supervisor
2001 - 2003	Electrostatic studies in proteins Supervisor	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 Co-supervisor of Carlos Manuel Alves da Costa Cunha	Bioquímica (PhD) Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2000/09 - 2001/09	Modelação molecular da interacção de proteínas em Desulfovibrio gigas Supervisor	Universidade de Coimbra, Portugal
1998/09 - 2000/11	Modelação e estudos de docking na transtirretina de dourada, Sparus aurata Supervisor	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 Supervisor	Universidade do Algarve, Portugal
2000 - 2000	Modelling Sidechain Conformations in Proteins Co-supervisor of Joaquim Pires Antunes Mendes	Bioquímica (PhD) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Event organisation

	Event name Type of event (Role)	Institution / Organization
2022/07/09 - 2022/07/14	IUBMB-FEBS-PABMB Biochemistry Congress (2022 - 2022) Congress (Member of the Organising Committee)
2021/10/14 - 2021/10/16	XXI SPB – National Congress of Biochemistry (2021 - 2021) Congress (Member of the Scientific Committee)	Universidade de Évora, Portugal
2021/06/14 - 2021/06/16	7th International Iberian Biophysics Congress (2021 - 2021) Congress (Member of the Organising Committee)
2019/03 - 2019/04	12th International Conference on Hydrogenases, Lisbon, Portugal (2019/03/31 - 2019/04/04) Conference (Member of the Organising Committee)
2018/06 - 2018/06	6th International Iberian Biophysics Congress and X Iberoamerican Congress of Biophysics, Castellón, Spain (2018/06/20 - 2018/06/22) Congress (Member of the Scientific Committee)
2017/07 - 2017/07	XXV National Meeting of the Portuguese Chemical Society, Lisboa, Portugal (2017/07/16 - 2017/07/19) Meeting (Member of the Organising Committee)	Sociedade Portuguesa de Química, Portugal
2017/07 - 2017/07	19th IUPAB congress and 11th EBSA congress, Edinburgh, Scotland (2017/07/16 - 2017/07/20) Congress (Member of the Scientific Committee)
2016/12 - 2016/12	XIX National Congress of Biochemistry, Guimarães, Portugal (2016/12/08 - 2016/12/10) Congress (Member of the Scientific Committee)
2016/06 - 2016/06	5th Iberian Biophysics Congress EBSA, Porto, Portugal (2016/06/15 - 2016/06/17) Congress (Member of the Organising Committee)
2013/07 - 2013/07	9th European Biophysics Congress EBSA (European Biophysical Societies Association), Lisbon, Portugal (2013/07/13 - 2013/07/17) Congress (Member of the Organising Committee)
2012/01 - 2012/01	Jornadas de Bioinformática 2012, Barcelona, Spain (2012/01/23 - 2012/01/25) Other (Member of the Scientific Committee)
2011/11 - 2011/11	10th Short course of the Portuguese Biophysical Society "Nanosciences for Life", Santarém, Portugal (2011/11/17 - 2011/11/19) Other (Other)	Sociedade Portuguesa de Biofísica, Portugal
2010/12 - 2010/12	Congresso Nacional de Bioquímica 2010, Porto, Portugal (2010/12/15 - 2010/12/17) Congress (Member of the Scientific Committee)
2010/10 - 2010/10	Xth Spanish Symposium on Bioinformatics (JBI2010), Malaga, Spain (2010/10/27 - 2010/10/29) Symposium (Member of the Scientific Committee)
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) Other (Member of the Organising Committee)	Sociedade Portuguesa de Biofísica, Portugal
2010/07 - 2010/07	IV Spanish-Portuguese Biophysical Congress, Zaragoza, Spain (2010/07/07 - 2010/07/10) Congress (Member of the Scientific Committee)
2009/10 - 2009/11	8th Short course of the Portuguese Biophysical Society "Systems Biology", Santarém, Portugal (2009/10/30 - 2009/11/01) Other (Member of the Organising Committee)	Sociedade Portuguesa de Biofísica, Portugal
2008/09 - 2008/09	Workshop “Structure, dynamics, and function of proteins”, Oeiras, Portugal (2008/09/17 - 2008/09/19) Workshop (Member of the Organising Committee)
2008/07 - 2008/07	1st Portuguese-Spanish-British Joint Biophysics Congress 2008, Lisbon, Portugal (2008/07/10 - 2008/07/13) Congress (President of the Organising Committee)
2007/10 - 2007/10	7th Short course of the Portuguese Biophysical Society "Biospectroscopy and Imaging", Santarém, Portugal (2007/10/19 - 2007/10/21) Other (Member of the Organising Committee)	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) Meeting (Member of the Organising Committee)
2006/09 - 2006/09	VI Ibero-American Congress of Biophysics, Madrid, Spain (2006/09/24 - 2006/09/27) Congress (Member of the Organising Committee)
2006/07 - 2006/07	8th European Biological Chemistry Conference, EUROBIC 8, Aveiro, Portugal (2006/07/02 - 2006/07/06) Conference (Member of the Organising Committee)
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) Other (Member of the Organising Committee)	Sociedade Portuguesa de Biofísica, Portugal
2004/10 - 2004/11	3rd Portuguese-Spanish Biophysics Congress, Lisbon, Portugal (2004/10/29 - 2004/11/01) Congress (President of the Organising Committee)
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) Other (Member of the Organising Committee)	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) Other	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) Other (Member of the Organising Committee)	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) Other (President of the Organising Committee)	Sociedade Portuguesa de Biofísica, Portugal

Jury of academic degree

	Topic Role	Candidate name (Type of degree) Institution / Organization
2021/07	Computational Studies Addressed to PLP-Dependent Enzymes (Thesis) Main arguer	Henrique Silva Fernandes (PhD) Universidade do Porto, Portugal
2021/06	Studies on the function and substrate permeation in ABC transporters by biomolecular simulations Supervisor	Bárbara Abreu (PhD) 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 (Thesis) Main arguer	Samina Kausar (PhD) Universidade de Lisboa Faculdade de Ciências, Portugal
2018/03	Anion transmembrane transport by synthetic molecules: a molecular modelling investigation (Thesis) Main arguer	Igor Oliveira Marques (PhD) Universidade de Aveiro, Portugal
2017/12	Computational design and experimental characterization of metallopeptides as proteases for bioengineering applications (Thesis) Main arguer	Henrique Daniel Figueiredo Carvalho (PhD) 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 (Thesis) Main arguer	João Pedro do Vale Hipólito Cavalheiro (Master) Universidade de Lisboa Instituto Superior Técnico, Portugal
2015/12	Molecular modelling and simulation of pH effects in lipid bilayers (Thesis) Main arguer	Diogo Ruivo dos Santos Vila Viçosa (PhD) 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 (Thesis) Main arguer	Hugo Alexandre Louro Filipe (PhD) Hospitais da Universidade de Coimbra, Portugal
2013/09	Constant-pH MD simulations of higher complexity lipid bilayer models: PA/PC binary mixtures (Thesis) Main arguer	Hugo Alexandre Feiteira dos Santos (Master) Universidade de Lisboa Faculdade de Ciências, Portugal
2012/12	Virtual screening with sense and sensibility in the search of new amyloid inhibitors (Thesis) Main arguer	Carlos J. V. Simões (PhD)
2012/07	Reductive scavenging of reactive oxygen species in prokaryotes (Thesis) Arguer	Ana Filipa Pinto (PhD) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2012/03	Propriedades electrónicas de espécies hidrofóbicas micro-solvatadas e em solução (Thesis) Arguer	Maria Margarida Pires dos Santos Mateus (PhD) Universidade de Lisboa Faculdade de Ciências, Portugal
2011/01	Characterization of the activity of nitrous oxide reductase: biochemical, spectroscopic and mimetic approaches (Thesis) Main arguer	Simone Dell’Acqua (PhD) Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2010/11	Molecular modelling of ABC transporter: from ATP hydrolysis to substrate transport (Thesis) Arguer	Ana Sofia Oliveira (PhD) 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 (Thesis) Main arguer	Nuno Ricardo Santos Loureiro da Silva Ferreira (PhD) Universidade de Coimbra, Portugal
2010/11	Search based methods for protein structure prediction (Thesis) Main arguer	Miguel Mourão Fialho Bugalho (PhD) 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 (Thesis) Main arguer	João Miguel Calado da Silva Freire (Master) Universidade de Lisboa Faculdade de Ciências, Portugal
2010/06	Theoretical study of the reactivity and energetics of organic radicals (Thesis) Arguer	Filipe Miguel Peres Agapito (PhD) Universidade de Lisboa Faculdade de Ciências, Portugal
2010/04	CotA-laccase from Bacillus subtilis: structure-function studies of catalytic copper centers (Thesis) Arguer	Paulo Jorge Rêgo Durão (PhD) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2010/01	Modelação molecular de associações entre aniões e receptors sintéticos (Thesis) Main arguer	Sérgio Miguel Fernandes dos Santos (PhD) 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 (Thesis) Arguer	Sara Isabel Rodrigues Rasteiro de Campos (PhD) 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 (Thesis) Main arguer	Marco André Coelho das Neves (PhD) Universidade de Coimbra, Portugal
2008/12	Ligações de hidrogénio: estudo de alguns aspectos energéticos, electrónicos e dinâmicos por primeiros princípios (Thesis) Arguer	Sílvia da Conceição Gomes Estácio (PhD) Universidade de Lisboa Faculdade de Ciências, Portugal
2008/05	Study of CFTR mutants and their processing properties: structural implications (Thesis) Arguer	Luísa Maria da Silva Pissarra (PhD) Universidade de Lisboa Faculdade de Ciências, Portugal
2007/10	Superoxide defence strategies in anaerobic prokariotes: The mechanism of superoxide reductases (Thesis) Arguer	João Vieira Rodrigues (PhD) 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 President of the jury	David Guerra Aragão (PhD) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2007/10	Enzyme structure and function in nonaqueous solvents (Thesis) Arguer	Nuno Miguel da Silva Micâelo (PhD)
2007/10	Molecular modelling of redox proteins involved in the oxygen and nitric oxide metabolism (Thesis) Arguer	Bruno Lourenço da Silva Victor (PhD) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2007/05	Regulation of arabinose metabolism in Bacillus subtilis. Linking structure and function (Thesis) Arguer	Irina Saraiva Franco (PhD) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2007/03	A non-assigned herpesvirus gene inducing cell cycle arrest and apoptosis President of the jury	Rute Nascimento (PhD) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2007/03	Hydrogen metabolism in Desulfovibrio vulgaris Hildenborough (Thesis) Arguer	Ana Filipa de Matos Almeida Valente (PhD) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2007/02	The Role of Flavodiiron Proteins in Nitric Oxide Detoxification (Thesis) Arguer	João Filipe Bogalho Vicente (PhD) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2007/02	Molecular modelling of redox proteins involved in the hydrogen metabolism (Thesis) Arguer	Vitor Hugo Oliveira Teixeira (PhD) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2006/12	Thermodynamic and kinetic characterisation of multiheme cytochromes (Thesis) Arguer	Catarina Morais Vaz Paquete (PhD) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2005/12	Assembly of the Bacillus subtilis spore coat (Thesis) Arguer	Teresa Vasconcelos Costa (PhD) 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 (Thesis) Main arguer	João Filipe Viegas Barroso (PhD) Universidade de Coimbra, Portugal
2004/06	Study of the localization of fucosyltransferase III. Importance of the transmembrane and cytosolic domains (Thesis) Arguer	Vitor Lino Sousa (PhD) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2003/12	Integrating protein structural information (Thesis) Main arguer	Ludwig Krippahl (PhD) 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 (Thesis) Arguer	Carlos Manuel Alves da Costa Cunha (PhD) 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 (Thesis) Arguer	Isabel Maria Travassos de Almeida de Jesus Bento (PhD) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2002/10	Protein stabilisation by diglycerol phosphate, a compatible solute from hyperthermophiles (Thesis) Arguer	Pedro Miguel Lamosa (PhD)
2001/11	Simulação de interacções intermoleculares em sistemas de interesse farmacológico (Thesis) Main arguer	Elsa Fernanda de Sousa Henriques (PhD) 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) (Thesis) Main arguer	Carla Sofia de Oliveira Ferreira (Master) 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 (Thesis) Main arguer	Miguel Xavier Jesus Josefat Fernandes (PhD) Universidade de Lisboa Faculdade de Ciências, Portugal
2000/07	Modelling sidechain conformation in proteins Supervisor	Joaquim Pires Antunes Mendes (PhD)

Association member

	Society Organization name	Role
1994 - Current	Portuguese Biochemical Society
1994 - Current	Portuguese Biophysical Society
1994 - Current	Portuguese Chemical Society
1994 - Current	The Biophysical Society (USA)

Committee member

	Activity description Role	Institution / Organization
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 Member	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 Member	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” Member	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 Member	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 Member	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 Member
2008/12 - 2008/12	Member of the selection committee for a Research position (Investigador Auxiliar) of FFUC Member	Universidade de Coimbra Faculdade de Farmácia, Portugal
2008/10 - 2008/10	Member of the selection committee for a Research position (Investigador Auxiliar) of FCUL Member	Universidade de Lisboa Faculdade de Farmácia, Portugal
2007/09 - 2007/10	Member of the selection committee for a Research position (Investigador Auxiliar) of FFUL Member	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 Member
2006/06 - 2006/06	Member of the selection committee for a Research position (Investigador Auxiliar) of ITQB-UNL Member	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 Member	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 Member
2003/10 - 2003/10	Member of the selection committee for four Research positions of the Associated Laboratory ITQB/IGC/IBET Member
2003/09 - 2003/09	Member of the selection committee for the Research position in Protein Crystallography of the Associated Laboratory REQUIMTE (FCT-UNL, Portugal) Member	REQUIMTE Unidade de Ciências Biomoleculares Aplicadas, Portugal

Course / Discipline taught

	Academic session	Degree Subject (Type)	Institution / Organization
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, Brazil
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, Brazil
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

Other jury / evaluation

	Activity description	Institution / Organization
2018 - Current	Member the Editorial Board of the FEBS Open Bio Journal
2013 - Current	Member the Editorial Board of the Scientific Reports Journal
2012 - Current	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, Czech Republic
2020 - 2021	Member of the International Review Panel evaluating research proposals for the National Science Centre	National Science Centre, Poland
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, Poland
2017 - 2017	Evaluation of one project from the Deutsche Forschungsgemeinschaft (German Research Foundation) on the Emmy Noether Programme	Deutsche Forschungsgemeinschaft, Germany
2017 - 2017	Evaluation one individual proposal (36 months) from the Deutsche Forschungsgemeinschaft (German Research Foundation)	Deutsche Forschungsgemeinschaft, Germany
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, Poland
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, Poland
2013 - 2013	Evaluation of one project for the Austrian Science Fund	Fonds zur Förderung der wissenschaftlichen Forschung, Austria
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, United States
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, United States
2011 - 2011	Evaluation of a project from the Emmy Noether-Programm Nachwuchsgrupper Neuantrag	Deutsche Forschungsgemeinschaft, Germany
2011 - 2011	Evaluation of two projects for the Austrian Science Fund	Fonds zur Förderung der wissenschaftlichen Forschung, Austria
2011 - 2011	Evaluation of two research projects for the Cyprus Research Promotion Foundation	Cyprus Research Promotion Foundation, Cyprus
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, Netherlands
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, Czech Republic
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

Distinctions

Other distinction

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