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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 and viral membrane fusion proteins 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. A lot of work is centred on redox proteins (cytochromes, haem-copper oxidases, laccases, hydrogenases), but the lab is also doing modelling work in other areas, namely in molecular mechanisms in ABC transporters, haemagglutinin mediated membrane fusion and enzymes in non-aqueous solvents. 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

  • Ana Sofia Oliveira, Post-doc

  • Diana Lousa, Post-doc

  • Francisco Fernandes, Post-doc (also affiliated with IST, Universidade de Lisboa)

  • João M. Damas, PhD student

  • Carla Baltazar, PhD student

  • David Cruz, PhD student

  • Bárbara Abreu, PhD student

  • Tiago Resende, PhD student (also affiliated with Universidade do Minho)

  • Tiago Barbosa, Research student


Selected Publications

  1. 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.
  2. 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.
  3. Oliveira, ASF, Damas, JM, Baptista, AM, Soares, CM (2014) “Exploring O2 diffusion in A-type Cytochrome c Oxidases: molecular dynamics simulations uncover two alternative channels towards the binuclear site, PLoS Comp.Biol., 10, e1004010


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 experimental. 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, fusão de membranas de virús e enzimas em solventes não aquosos.


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