Implicit solvation in the self-consistent mean field theory method: sidechain modelling and prediction of folding free energies of protein mutants. - Joaquim Mendes; António M. Baptista; Maria Arménia Carrondo; Cláudio M. Soares (J. Comput. Aided Mol. Des., 2001)

Inter-domain Communication Mechanisms in an ABC Importer: A Molecular Dynamics Study of the MalFGK2E Complex. - A. Sofia F. Oliveira; António M. Baptista; Cláudio M. Soares (PLoS Comput. Biol., 2011)

Analyzing the Molecular Basis of Enzyme Stability in Ethanol/Water Mixtures Using Molecular Dynamics Simulations. - Diana Lousa; António M. Baptista; Cláudio M. Soares (J. Chem. Inf. Model., 2012)

Structural Determinants for the Membrane Insertion of the Transmembrane Peptide of Hemagglutinin from Influenza Virus. - Bruno L. Victor; António M. Baptista; Cláudio M. Soares (J. Chem. Inf. Model., 2012)

Exploring O2 Diffusion in A-Type Cytochrome c Oxidases: Molecular Dynamics Simulations Uncover Two Alternative Channels towards the Binuclear Site. - A. Sofia F. Oliveira; João M. Damas; António M. Baptista; Cláudio M. Soares (PLoS Comput. Biol., 2014)

Self-Assembly Molecular Dynamics Simulations Shed Light into the Interaction of the Influenza Fusion Peptide with a Membrane Bilayer. - Bruno L. Victor; Diana Lousa; Jorge M. Antunes; Cláudio M. Soares (J. Chem. Inf. Model., 2015)

Effect of a pH Gradient on the Protonation States of Cytochrome c Oxidase: A Continuum Electrostatics Study. - Pedro R. Magalhães; A. Sofia F. Oliveira; Sara R. R. Campos; Cláudio M. Soares; António M. Baptista (J. Chem. Inf. Model., 2017)