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Cláudio M. Soares Lab


The Protein Modelling Laboratory works on molecular modelling of proteins using computational biophysical methods. Redox proteins, ABC transporters, viral membrane fusion proteins and enzyme engineering are some examples of the work developed

Cláudio M. Soares

PhD 1994 in Theoretical Biochemistry, Univ. Lisboa / Uppsala University

Phone (+351) 214469259 / (+351) 214469610

Extension 1259/1610


Research Interests

The Protein Modelling Laboratory works on molecular modelling of proteins using computational biophysical methods. Its members have experience in a quite large number of areas, from basic research in methods, to applications with biotechnological and biomedical interest. Since its inception, the laboratory has traditionally worked on redox proteins (cytochromes, haem-copper oxidases, laccases, hydrogenases), but new areas of work have been added along the years. The ones that are still active nowadays comprise, among others, studies of the molecular mechanisms in ABC transporters, the understanding of membrane fusion processes mediated by viral proteins and enzyme engineering for the creation of value added compounds. Besides its own research objectives, the Protein Modelling Group has extensive collaborations with many experimental groups, and together, aims at understanding Life at the molecular and atomic levels, from its smallest components to large supramolecular assemblies.


Group Members

  • Diana Lousa, Researcher

  • Caio Silva Souza, Post-doc

  • Carlos Cruz, Post-doc

  • Rozangela Pedrosa, Visiting Professor

  • David Cruz, PhD student

  • Bárbara Abreu, PhD student

  • Joana Oliveira, PhD student (also affiliated with Isabel Rocha’s Laboratory

  • Cesar Pimenta, PhD student

  • Mariana Valério, PhD student

  • André Marques, Master student


Selected Publications

  1. Abreu, B, Lopes, EF, Oliveira, ASF, Soares, CM (2020) “The mutation F508del disturbs the dynamics of the nucleotide binding domains of CFTR before and after ATP hydrolysis”, Proteins, 88, 113-126

  2. Kaur, H, Abreu, B, Akhmetzyanov, D, Lakatos-Karoly, A; Soares, CM, Prisner, T, Glaubitz, C (2018) “Unexplored nucleotide binding modes for the ABC exporter MsbA”, JACS, 140, 14112–14125

  3. Jeremias, HF, Lousa, D, Hollmann, A, Coelho, AC, Baltazar, CS, Seixas, JD, Marques, AR, Santos, NC, Romão, CC, Soares, CM (2018) “Study of the interactions of bovine serum albumin with a molybdenum(II) carbonyl complex by spectroscopic and molecular simulation methods”, PLOS One, 13(9): e0204624

  4. Lousa, D, Pinto, ART, Victor, BL, Laio, A, Veiga, AS, Castanho, MARB, Soares, CM (2016) “Fusing simulation and experiment: The effect of mutations on the structure and activity of the influenza fusion peptide”, Sci.Rep., 6, 28099.

  5. Oliveira, ASF, Campos, SRR, Baptista, AM, Soares, CM (2016) “Coupling between protonation and conformation in cytochrome c oxidase: Insights from Constant-pH MD simulations”, BBA Bioenergetics, 1857, 759-771.



Laboratory's Website

For further information please visit the laboratory's website


Modelação de Proteínas  (PT)

O Laboratório de Modelação de Proteínas desenvolve investigação na área da simulação física de proteínas, tentando compreender processos biológicos utilizando meios computacionais, ou em colaboração com grupos de investigação experimentais. O objectivo final destas investigações é a compreensão da Vida ao nível molecular e atómico, pela simulação dos seus mais pequenos componentes. O trabalho do Laboratório de Modelação de Proteínas centra-se no estudo de proteínas envolvidas em cadeias transportadoras de electrões, transportadores ABC, proteínas virais envolvidas em fusão de membranas e engenharia de enzimas para a produção de compostos de valor acrescentado.


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