Inclusion of conserved buried water molecules in the model structure of rat submaxillary kallikrein. - Elsa F. Henriques; Maria João Ramos; Christopher A. Reynolds (J. Comput. Aided Mol. Des., 1998)

Byte Structure Variable Length Coding (BS-VLC): A New Specific Algorithm Applied in the Compression of Trajectories Generated by Molecular Dynamics. - André Melo; André T. Puga; Fernanda Gentil; Nelson Brito; Artur Pimenta Alves; Maria João Ramos (J. Chem. Inf. Comput. Sci., 2000)

The search for a new model structure of beta-Factor XIIa. - Elsa S. Henriques; Wely B. Floriano; Nathalie Reuter; André Melo; David Brown 001; José A. N. F. Gomes; Bernard Maigret; Marco A. C. Nascimento; Maria João Ramos (J. Comput. Aided Mol. Des., 2001)

New designs for MRI contrast agents. - Pedro Alexandrino Fernandes; Alexandra T. P. Carvalho; A. T. Marques; A. L. F. Pereira; A. P. S. Madeira; Ana Sofia P. Ribeiro; A. F. R. Carvalho; E. T. A. Ricardo; F. J. V. Pinto; Hélder A. Santos; H. D. G. Mangericão; H. M. Martins; et al. (J. Comput. Aided Mol. Des., 2003)

A molecular modeling study of inhibitors of nuclear factor kappa-B (p50) - DNA binding. - Vineet Pande; Rakesh K. Sharma; Jun-Ichiro Inoue; Masami Otsuka; Maria João Ramos (J. Comput. Aided Mol. Des., 2003)

Computational studies of new potential antimalarial compounds - Stereoelectronic complementarity with the receptor. - César Portela; Carlos M. M. Afonso; Madalena M. M. Pinto; Maria João Ramos (J. Comput. Aided Mol. Des., 2003)

Ribonucleotide activation by enzyme ribonucleotide reductase: Understanding the role of the enzyme. - Nuno M. F. S. A. Cerqueira; Pedro Alexandrino Fernandes; Leif A. Eriksson; Maria João Ramos (J. Comput. Chem., 2004)

Theoretical study of ribonucleotide reductase mechanism-based inhibition by 2-azido-2-deoxyribonucleoside 5-diphosphates. - Susana Pereira; Pedro Alexandrino Fernandes; Maria João Ramos (J. Comput. Chem., 2004)

Mechanism for ribonucleotide reductase inactivation by the anticancer drug gemcitabine. - Susana Pereira; Pedro Alexandrino Fernandes; Maria João Ramos (J. Comput. Chem., 2004)

Determination of the pKa between the active site cysteines of thioredoxin and DsbA. - Alexandra T. P. Carvalho; Pedro Alexandrino Fernandes; Maria João Ramos (J. Comput. Chem., 2006)

QM/QM study of the coverage effects on the adsorption of amino-cyclopentene at the Si(100) surface. - Hugo R. R. Santos; Gregori Ujaque; Maria João Ramos; José A. N. F. Gomes (J. Comput. Chem., 2006)

Computational alanine scanning mutagenesis - An improved methodological approach. - Irina S. Moreira; Pedro Alexandrino Fernandes; Maria João Ramos (J. Comput. Chem., 2007)

Theoretical studies on farnesyl transferase: Evidence for thioether product coordination to the active-site zinc sphere. - Sérgio Filipe Sousa; Pedro Alexandrino Fernandes; Maria João Ramos (J. Comput. Chem., 2007)

Mechanistic studies on the formation of glycosidase-substrate and glycosidase-inhibitor covalent intermediates. - Natércia F. Brás; Sara A. Moura-Tamames; Pedro Alexandrino Fernandes; Maria João Ramos (J. Comput. Chem., 2008)

Role of the variable active site residues in the function of thioredoxin family oxidoreductases. - Alexandra T. P. Carvalho; Pedro Alexandrino Fernandes; Marcel Swart; Joost N. P. Van Stralen; Friedrich Matthias Bickelhaupt; Maria João Ramos (J. Comput. Chem., 2009)

Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for zinc complexes. - Sérgio Filipe Sousa; Emanuela S. Carvalho; Diana M. Ferreira; Isabel S. Tavares; Pedro Alexandrino Fernandes; Maria João Ramos; José A. N. F. Gomes (J. Comput. Chem., 2009)

Protein-protein docking dealing with the unknown. - Irina S. Moreira; Pedro Alexandrino Fernandes; Maria João Ramos (J. Comput. Chem., 2010)

Parameters for molecular dynamics simulations of iron-sulfur proteins. - Alexandra T. P. Carvalho; Ana F. S. Teixeira; Maria João Ramos (J. Comput. Chem., 2013)

Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for copper complexes. - Sérgio Filipe Sousa; Gaspar R. P. Pinto; António J. M. Ribeiro; João T. S. Coimbra; Pedro Alexandrino Fernandes; Maria João Ramos (J. Comput. Chem., 2013)

AutoDock4Zn: An Improved AutoDock Force Field for Small-Molecule Docking to Zinc Metalloproteins. - Diogo Santos-Martins; Stefano Forli; Maria João Ramos; Arthur J. Olson (J. Chem. Inf. Model., 2014)

Calculation of distribution coefficients in the SAMPL5 challenge from atomic solvation parameters and surface areas. - Diogo Santos-Martins; Pedro Alexandrino Fernandes; Maria João Ramos (J. Comput. Aided Mol. Des., 2016)

New Parameters for Higher Accuracy in the Computation of Binding Free Energy Differences upon Alanine Scanning Mutagenesis on Protein-Protein Interfaces. - Inês C. M. Simões; Inês P. D. Costa; João T. S. Coimbra; Maria João Ramos; Pedro Alexandrino Fernandes (J. Chem. Inf. Model., 2017)

molUP: A VMD plugin to handle QM and ONIOM calculations using the gaussian software. - Henrique S. Fernandes; Maria João Ramos; Nuno M. F. S. A. Cerqueira (J. Comput. Chem., 2018)

Assessing the validity of DLPNO-CCSD(T) in the calculation of activation and reaction energies of ubiquitous enzymatic reactions. - Pedro Paiva; Maria João Ramos; Pedro Alexandrino Fernandes (J. Comput. Chem., 2020)

Role of Enzyme and Active Site Conformational Dynamics in the Catalysis by α-Amylase Explored with QM/MM Molecular Dynamics. - Rui P. P. Neves; Pedro Alexandrino Fernandes; Maria João Ramos (J. Chem. Inf. Model., 2022)

Transmembrane Protease Serine 2 Proteolytic Cleavage of the SARS-CoV-2 Spike Protein: A Mechanistic Quantum Mechanics/Molecular Mechanics Study to Inspire the Design of New Drugs To Fight the COVID-19 Pandemic. - Luís M. C. Teixeira; João T. S. Coimbra; Maria João Ramos; Pedro Alexandrino Fernandes (J. Chem. Inf. Model., 2022)

Engineering DszC Mutants from Transition State Macrodipole Considerations and Evolutionary Sequence Analysis. - Rui P. P. Neves; Maria João Ramos; Pedro Alexandrino Fernandes (J. Chem. Inf. Model., 2023)

Unraveling the Reaction Mechanism of Russell's Viper Venom Factor X Activator: A Paradigm for the Reactivity of Zinc Metalloproteinases? - Juliana Castro-Amorim; Ana Oliveira; Ashis K. Mukherjee; Maria João Ramos; Pedro Alexandrino Fernandes (J. Chem. Inf. Model., 2023)

Deciphering the Catalytic Mechanism of Virginiamycin B Lyase with Multiscale Methods and Molecular Dynamics Simulations. - João T. S. Coimbra; Pedro Alexandrino Fernandes; Maria João Ramos (J. Chem. Inf. Model., 2023)

DszA Catalyzes C-S Bond Cleavage through N5-Hydroperoxyl Formation. - Pedro Ferreira; Rui P. P. Neves; Filipa P. Miranda; Ana V. Cunha; Remco W. A. Havenith; Maria João Ramos; Pedro Alexandrino Fernandes (J. Chem. Inf. Model., 2024)