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PEDRO EDUARDO MARQUES LOPES. Concluiu o(a) Doutoramento em Química em 2000 pela Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica. É Investigador Auxiliar (carreira) na Fundação da Faculdade de Ciências da Universidade de Lisboa. Publicou mais de 40 artigos em revistas especializadas. Possui 2 capítulos de livros. Possui 3 patentes registadas. Participou como Investigador em varios projetos. Atua na área de Ciências Exatas com ênfase em Química Computacional e Teórica com aplicações em Bioquímica. Nas suas atividades profissionais interagiu com multiplos colaboradores em coautorias de trabalhos científicos. No seu currículo Ciência Vitae os termos mais frequentes na contextualização da produção científica, tecnológica e artístico-cultural são: Quantum Mechanics; Tight-Binding; ab initio; Semi-Empirical; Classical Force Fields; Molecular Dynamics; Proteins; Drug-Discovery; Molecular Modeling; DFT; Docking; Lead-Optimization; Polarization. Os trabalhos ciêntíficos mais relevantes são o algorítmo mais rápido alguma vez desenvolvido para o cálculo de Integrais de Repulsão Electrónica e vários campos de forçcas no âmbito do CHARMM, incluíndo o campo de forças Drude com polarização para proteínas.
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Identificação

Identificação pessoal

Nome completo
Pedro Eduardo Marques Lopes

Nomes de citação

  • Lopes, Pedro E. M.

Identificadores de autor

Ciência ID
2F17-AC1A-8632
ORCID iD
0000-0002-7383-7886

Endereços de correio eletrónico

  • pemlopes@fastcompchem.pt (Profissional)

Moradas

  • UBIMedical - Estrada Municipal 506, 6200-284, Covilhã, Covilhã, Portugal (Profissional)

Websites

Domínios de atuação

  • Ciências Exatas - Química
Formação
Grau Classificação
2000
Concluído
 Química (Doutoramento)
Especialização em Especialidade: Química
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
"Electronic Structure and Reactivity of Transition Metal Complexes" (TESE/DISSERTAÇÃO)
Percurso profissional

Ciência

Categoria Profissional
Instituição de acolhimento 		Empregador
2019/01/21 - 2020/04/30 Investigador Auxiliar (carreira) (Investigação) Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal

Docência no Ensino Superior

Categoria Profissional
Instituição de acolhimento 		Empregador
2011/08/01 - 2014/07/31 Professor Auxiliar (Docente Universitário) School of Pharmacy, University of Maryland Baltimore, Estados Unidos

Outros

Categoria Profissional
Instituição de acolhimento 		Empregador
2019/07 - Atual Chief Scientist, Founder FastCompChem, Lda, Portugal
FastCompChem, Lda, Portugal
Projetos

Bolsa

Designação Financiadores
2024/02 - 2028/01 QUANTUM-TOX - Revolutionizing Computational Toxicology with Electronic Structure Descriptors andArtificial Intelligence
101130724
 European Commission

Projeto

Designação Financiadores
2007/07/01 - 2015/06/30 Polarizable Force Field for Proteins and Lipids
5R01GM072558-11
Investigador
University of Maryland Baltimore, Estados Unidos
Concluído
2007/07 - 2015/06 Polarizable Force Field for Proteins and Lipids
5R01GM072558-11
 N/A
Produções

Publicações

Artigo em boletim informativo
  1. Lopes, Pedro E. M.. "New Born-Oppenheimer molecular dynamics based on the extended Hückel method: first results and future developments", 2018, https://arxiv.org/abs/1810.07680.
Artigo em conferência
  1. Lopes, Pedro E. M.. "Renaissance of semi-empirical methods: Fast computation of 2-electron integrals". Trabalho apresentado em 254th Meeting of the American Chemical Society, Washington, DC, 2017.
  2. Lopes, Pedro E. M.. "Fast Calculation of Two-Electron Integrals: a Numerical Approach". Trabalho apresentado em 249th Meeting of the American Chemical Society, Denver, CO, 2015.
  3. Lopes, Pedro E. M.; Mackerell, Alexander D., Jr.. "Current Status of the CHARMM Classical Drude Oscillator Polarizable Force Field for Proteins". Trabalho apresentado em 244th Meeting of the American Chemical Society, Philadelphia, PA, 2012.
  4. He, Xibing; Lopes, Pedro E. M.; Mackerell, Alexander D., Jr.. "Development of a CHARMM Polarizable Force Field for Aldehydes, Ketones, Acyclic Polyalcohols, and Acyclic Monosaccharides Using the Drude Oscillator Model". Trabalho apresentado em 244th Meeting of the American Chemical Society, 2012.
  5. Lopes, Pedro E. M.; Zhu, Xiao; MacKerell, Alexander D., Jr.. "pKa Calculations of Protein Side Chains in Explicit Solvent Using the Classical Drude Polarizable Force Field". 2012.
  6. Lopes, Pedro. "Testing and validation of the newly developed drude polarizable force field for CHARMM". Trabalho apresentado em The 238th ACS National Meeting, 2009.
Artigo em revista
  1. de Matos AM; Blázquez-Sánchez MT; Bento-Oliveira A; de Almeida RFM; Nunes R; Lopes PEM; Machuqueiro M; et al. "Glucosylpolyphenols as Inhibitors of Aß-Induced Fyn Kinase Activation and Tau Phosphorylation: Synthesis, Membrane Permeability, and Exploratory Target Assessment within the Scope of Type 2 Diabetes and Alzheimer's Disease.". Journal of medicinal chemistry (2020): http://europepmc.org/abstract/med/32959649.
    10.1021/acs.jmedchem.0c00841
  2. Lopes, Pedro E.M.. "Fast Simulation Methods for Chemistry and Biology Based on Quantum Mechanics". Biophysical Journal 116 3 (2019): 140a. http://dx.doi.org/10.1016/j.bpj.2018.11.778.
    10.1016/j.bpj.2018.11.778
  3. Fang-Yu Lin; Pedro E. M. Lopes; Edward Harder; Benoît Roux; Alexander D. MacKerell, Jr.. "Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator". Journal of Chemical Information and Modeling (2018): https://doi.org/10.1021/acs.jcim.8b00132.
    10.1021/acs.jcim.8b00132
  4. Lopes, Pedro E. M.. "Fast calculation of two-electron-repulsion integrals: a numerical approach". Theoretical Chemistry Accounts 136 9 (2017): 112-112. https://doi.org/10.1007/s00214-017-2142-7.
    10.1007/s00214-017-2142-7
  5. Astudillo, Luisana; da Silva, Thiago G.; Wang, Zhiqiang; Han, Xiaoqing; Jin, Ke; VanWye, Jeffrey; Zhu, Xiaoxia; et al. "The small molecule IMR-1 inhibits the Notch transcriptional activation complex to suppress tumorigenesis". Cancer Research (2016): http://cancerres.aacrjournals.org/content/early/2016/04/13/0008-5472.CAN-16-0061.abstract.
    10.1158/0008-5472.CAN-16-0061
  6. Roux, Benoit; Li, Hui; Chowdhary, Janamejaya; Harder, Edward; Lopes, Pedro E.M.; Huang, Lei; MacKerell, Alexander D.. "Ion Channel Simulation with Explicit Solvent and Lipid Membrane Based on the Drude Polarizable Force Field". Biophysical Journal 106 2 (2014): 44a. http://dx.doi.org/10.1016/j.bpj.2013.11.319.
    Publicado • 10.1016/j.bpj.2013.11.319
  7. Lopes, Pedro E.M.; Huang, Jing; Shim, Jihyun; Luo, Yun; Li, Hui; Savelyev, Alexey; Patel, Dhilon; et al. "Development of a Polarizable Force Field for Macromolecules Based on the Classical Drude Oscillator". Biophysical Journal 106 2 (2014): 43a. http://dx.doi.org/10.1016/j.bpj.2013.11.318.
    10.1016/j.bpj.2013.11.318
  8. Huang, Jing; Lopes, Pedro E. M.; Roux, Benoît; MacKerell Jr, Alexander D.. "Recent advances in polarizable force fields for macromolecules: microsecond simulations of proteins using the classical Drude oscillator model". The journal of physical chemistry letters 5 18 (2014): 3144-3150. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000343067700003&KeyUID=WOS:000343067700003.
    10.1021/jz501315h
  9. Chowdhary, Janamejaya; Li, Hui; Harder, Ed; Lopes, Pedro; MacKerell, Alex; Roux, Benoit. "Drude Model Based Polarizable Force Field for Lipids". Biophysical Journal 104 2 (2013): 31a. http://dx.doi.org/10.1016/j.bpj.2012.11.210.
    10.1016/j.bpj.2012.11.210
  10. Li, Hui; Callahan, Karen; Mackerell, Alexander D.; Roux, Benoit. "Development of the Charmm Drude Polarizable Force Field for the Study of Ion Interactions in Biological Systems". Biophysical Journal 104 2 (2013): 507a. http://dx.doi.org/10.1016/j.bpj.2012.11.2799.
    10.1016/j.bpj.2012.11.2799
  11. Small, Meagan C.; Lopes, Pedro; Andrade, Rodrigo B.; MacKerell, Alexander D., Jr.. "Impact of Ribosomal Modification on the Binding of the Antibiotic Telithromycin Using a Combined Grand Canonical Monte Carlo/Molecular Dynamics Simulation Approach". Plos Computational Biology 9 6 (2013):
    10.1371/journal.pcbi.1003113
  12. Lin, Bin; Lopes, Pedro E. M.; Roux, Benoit; MacKerell, Alexander D., Jr.. "Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields". Journal of Chemical Physics 139 8 (2013):
    10.1063/1.4818731
  13. Chowdhary, Janamejaya; Harder, Edward; Lopes, Pedro E. M.; Huang, Lei; MacKerell, Alexander D., Jr.; Roux, Benoit. "A Polarizable Force Field of Dipalmitoylphosphatidylcholine Based on the Classical Drude Model for Molecular Dynamics Simulations of Lipids". Journal of Physical Chemistry B 117 31 (2013): 9142-9160.
    10.1021/jp402860e
  14. Yu, Wenbo; Lopes, Pedro E. M.; Roux, Benoit; MacKerell, Alexander D., Jr.. "Six-site polarizable model of water based on the classical Drude oscillator". Journal of Chemical Physics 138 3 (2013):
    10.1063/1.4774577
  15. Hom, Kellie; Heinzl, Geoffrey A.; Eakanunkul, Suntara; Lopes, Pedro E. M.; Xue, Fengtian; MacKerell, Alexander D., Jr.; Wilks, Angela. "Small Molecule Antivirulents Targeting the Iron-Regulated Heme Oxygenase (HemO) of P. aeruginosa". Journal of Medicinal Chemistry 56 5 (2013): 2097-2109.
    10.1021/jm301819k
  16. He, Xibing; Lopes, Pedro E. M.; MacKerell, Alexander D., Jr.. "Polarizable Empirical Force Field for Acyclic Polyalcohols Based on the Classical Drude Oscillator". Biopolymers 99 10 (2013): 724-738.
    10.1002/bip.22286
  17. Lopes, Pedro E. M.; Huang, Jing; Shim, Jihyun; Luo, Yun; Li, Hui; Roux, Benoit; MacKerell, Alexander D., Jr.. "Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator". Journal of Chemical Theory and Computation 9 12 (2013): 5430-5449.
    10.1021/ct400781b
  18. Zhu, Xiao; Lopes, Pedro E. M.; Shim, Jihyun; MacKerell, Alexander D., Jr.. "Intrinsic Energy Landscapes of Amino Acid Side-Chains". Journal of Chemical Information and Modeling 52 6 (2012): 1559-1572.
    10.1021/ci300079j
  19. Zhu, Xiao; Lopes, Pedro E. M.; Shim, Jihyun; MacKerell, Alexander D., Jr.. "Intrinsic Energy Landscapes of Amino Add Side-Chains (vol 52, pg 1559, 2012)". Journal of Chemical Information and Modeling 52 8 (2012): 2317-2318.
    10.1021/ci300301x
  20. Zhu, Xiao; Lopes, Pedro E. M.; MacKerell, Alexander D., Jr.. "Recent developments and applications of the CHARMM force fields". Wiley Interdisciplinary Reviews-Computational Molecular Science 2 1 (2012): 167-185.
    10.1002/wcms.74
  21. Best, Robert B.; Zhu, Xiao; Shim, Jihyun; Lopes, Pedro E. M.; Mittal, Jeetain; Feig, Michael; MacKerell, Alexander D., Jr.. "Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone phi, psi and Side-Chain chi(1) and chi(2) Dihedral Angles". Journal of Chemical Theory and Computation 8 9 (2012): 3257-3273.
    10.1021/ct3004000x
  22. Zhu, Xiao; Lopes, Pedro; Shim, Jihyun; MacKerell, Alexander D.. "Analysis of Amino Acid Sidechain Chi1, Chi2 Conformational Properties Using Quantum Mechanical and Experimental Crystallographic Survey Data". Biophysical Journal 100 3 (2011): 147a. http://dx.doi.org/10.1016/j.bpj.2010.12.1010.
    10.1016/j.bpj.2010.12.1010
  23. Lopes, Pedro E.M.; Zhu, Xiao; Lau, Albert; Roux, Benoit; MacKerell, Alexander D.. "Development of the Charmm Polarizable Force Field for Polypeptides Based on Drude Oscillators". Biophysical Journal 100 3 (2011): 612a. http://dx.doi.org/10.1016/j.bpj.2010.12.3527.
    10.1016/j.bpj.2010.12.3527
  24. Vanommeslaeghe, K.; Hatcher, E.; Acharya, C.; Kundu, S.; Zhong, S.; Shim, J.; Darian, E.; et al. "CHARMM General Force Field: A Force Field for Drug-Like Molecules Compatible with the CHARMM All-Atom Additive Biological Force Fields". Journal of Computational Chemistry 31 4 (2010): 671-690.
    10.1002/jcc.21367
  25. Baker, Christopher M.; Lopes, Pedro E. M.; Zhu, Xiao; Roux, Benoit; MacKerell, Alexander D., Jr.. "Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field". Journal of Chemical Theory and Computation 6 4 (2010): 1181-1198.
    10.1021/ct9005773
  26. West, Abby L.; St John, Franz; Lopes, Pedro E. M.; MacKerell, Alexander D., Jr.; Pozharski, Edwin; Michel, Sarah L. J.. "Holo-Ni(II)HpNikR Is an Asymmetric Tetramer Containing Two Different Nickel-Binding Sites". Journal of the American Chemical Society 132 41 (2010): 14447-14456.
    10.1021/ja104118r
  27. Lopes, Pedro E. M.; Demchuk, Eugene; Mackerell, Alexander D., Jr.. "Reconstruction of the (011) Surface on alpha-Quartz: A Semiclassical Ab Initio Molecular Dynamics Study". International Journal of Quantum Chemistry 109 1 (2009): 50-64.
    10.1002/qua.21726
  28. Lopes, Pedro E. M.; Roux, Benoit; MacKerell, Alexander D., Jr.. "Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability: theory and applications". Theoretical Chemistry Accounts 124 1-2 (2009): 11-28.
    10.1007/s00214-009-0617-x
  29. Lopes, Pedro E. M.; Lamoureux, Guillaume; Mackerell, Alexander D., Jr.. "Polarizable Empirical Force Field for Nitrogen-Containing Heteroaromatic Compounds Based on the Classical Drude Oscillator". Journal of Computational Chemistry 30 12 (2009): 1821-1838.
    10.1002/jcc.21183
  30. Lopes, Pedro E. M.; Lamoureux, Guillaume; Roux, Benoit; MacKerell, Alexander D., Jr.. "Polarizable empirical force field for aromatic compounds based on the classical drude oscillator". Journal of Physical Chemistry B 111 11 (2007): 2873-2885.
    10.1021/jp0663614
  31. Furci, Lena M.; Lopes, Pedro; Eakanunkul, Suntara; Zhong, Shijun; MacKerell, Alexander D., Jr.; Wilks, Angela. "Inhibition of the bacterial heme oxygenases from Pseudomonas aeruginosa and Neisseria meningitidis: Novel antimicrobial targets". Journal of Medicinal Chemistry 50 16 (2007): 3804-3813.
    10.1021/jm0700969
  32. Harder, Edward; Anisimov, Victor M.; Vorobyov, Igor V.; Lopes, Pedro E. M.; Noskov, Sergei Y.; MacKerell, Alexander D., Jr.; Roux, Benoit. "Atomic level anisotropy in the electrostatic modeling of lone pairs for a polarizable force field based on the classical Drude oscillator". Journal of Chemical Theory and Computation 2 6 (2006): 1587-1597.
    10.1021/ct600180x
  33. Lopes, P. E. M.; Murashov, V.; Tazi, M.; Demchuk, E.; MacKerell, A. D.. "Development of an empirical force field for silica. Application to the quartz-water interface". Journal of Physical Chemistry B 110 6 (2006): 2782-2792.
    10.1021/jp055341j
  34. Calhorda, Maria José; Lopes, Pedro E.M; Calhorda, M.J.; Lopes, P.E.M.. "An ‘atoms in molecules’ (AIM) analysis of the dihydrogen bond in organometallic compounds". Journal of Organometallic Chemistry 609 1-2 (2000): 53-59. http://dx.doi.org/10.1016/s0022-328x(00)00235-7.
    10.1016/s0022-328x(00)00235-7
  35. Calhorda, M.J.; Lopes, P.E.M.; Baerends, E.J.. "Insertion of isonitrile into the Mo-C bond of [MoCp2(CH3)(CNH)]+: A density functional study". New Journal of Chemistry 24 5 (2000): 289-293. http://www.scopus.com/inward/record.url?eid=2-s2.0-0034076596&partnerID=MN8TOARS.
    10.1039/b000485p
  36. Braga, D.; Grepioni, F.; Tedesco, E.; Calhorda, M.J.; Lopes, P.E.M.. "The effect of the counter ion on M - H···H - X (X = O, N) interactions in crystalline transition metal hydrides". New Journal of Chemistry 23 2 (1999): 219-226. http://www.scopus.com/inward/record.url?eid=2-s2.0-0032791515&partnerID=MN8TOARS.
    10.1039/a809073d
  37. Calhorda, M.J.; Lopes, P.E.M.; Schier, A.; Herrmann, R.. "Ferrocenylsilatranes: A synthetic, structural and theoretical investigation". Journal of Organometallic Chemistry 543 1-2 (1997): 93-102. http://www.scopus.com/inward/record.url?eid=2-s2.0-0031591914&partnerID=MN8TOARS.
  38. Calhorda, M.J.; Lopes, P.E.M.. "Bonding of acetone to Rh(111) and the effect of oxygen". Anales de Quimica 93 2 (1997): 119-124. http://www.scopus.com/inward/record.url?eid=2-s2.0-33749394691&partnerID=MN8TOARS.
  39. Wadepohl, H.; Calhorda, M.J.; Herrmann, M.; Jost, C.; Lopes, P.E.M.; Pritzkow, H.. "Organometallic cluster complexes with face-capping arene ligands. 8. Nucleophilic reactivity of cluster complexes with face-capping arene ligands: Metal vs ligand protonation". Organometallics 15 26 (1996): 5622-5634. http://www.scopus.com/inward/record.url?eid=2-s2.0-0006224970&partnerID=MN8TOARS.
  40. Calhorda, M.J.; Lopes, P.E.M.; Friend, C.M.. "Theoretical studies of ethylene adsorption and oxidation on clean and oxygen covered rhodium (111)". Journal of Molecular Catalysis. A, Chemical 97 3 (1995): 157-171. http://www.scopus.com/inward/record.url?eid=2-s2.0-0042062893&partnerID=MN8TOARS.
  41. Braga, D.; Grepioni, F.; Tedesco, E.; Calhorda, M. J.; Lopes, P. E. M.. "MOLECULAR-STRUCTURE AND CRYSTAL-STRUCTURE GENERATION FOR FE-3(CO)(12)". Journal of the Chemical Society-Dalton Transactions 20 (1995): 3297-3306.
    10.1039/dt9950003297
  42. Braga, D.; Grepioni, F.; Tedesco, E.; Calhorda, M.J.; Lopes, P.E.M.. "Molecular structure and crystal structure generation for [Fe3(CO)12]". Journal of the Chemical Society, Dalton Transactions 20 (1995): 3297-3306. http://www.scopus.com/inward/record.url?eid=2-s2.0-37049084359&partnerID=MN8TOARS.
    10.1039/DT9950003297
Capítulo de livro
  1. Lopes, Pedro E. M.; Guvench, Olgun; MacKerell, Alexander D.. "Current Status of Protein Force Fields for Molecular Dynamics Simulations". In Molecular Modeling of Proteins, 47-71. Springer New York, 2015.
    10.1007/978-1-4939-1465-4_3
  2. Lopes, Pedro E.M.; Harder, Edward; Roux, Benoît; Mackerell, Alexander D.. "Formalisms for the Explicit Inclusion of Electronic Polarizability in Molecular Modeling and Dynamics Studies". In Multi-scale Quantum Models for Biocatalysis, 219-257. Springer Netherlands, 2009.
    Publicado • 10.1007/978-1-4020-9956-4_9

Propriedade Intelectual

Patente
  1. Lopes, Pedro. 2013. "Heme oxygenase inhibitors, screening methods for heme oxygenase inhibitors and methods of use of heme oxygenase inhibitors for antimicrobial therapy".
  2. Lopes, Pedro. 2013. "Heme oxygenase inhibitors for the treatment of a microbial infection".
  3. Lopes, Pedro. 2009. "Heme oxygenase inhibitors and methods of therapeutic use".