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)

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)

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)

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)

A Weighted Constraint Optimization Approach to the Nurse Scheduling Problem. - Diogo Santos 002; Pedro Alexandrino Fernandes; Henrique Lopes Cardoso; Eugénio C. Oliveira (CSE, 2015)

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)

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)

A Computational and Modeling Study of the Reaction Mechanism of Staphylococcus aureus Monoglycosyltransferase Reveals New Insights on the GT51 Family of Enzymes. - Kenneth Goossens; Rui P. P. Neves; Pedro Alexandrino Fernandes; Hans De Winter (J. Chem. Inf. Model., 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)