Pedro Alexandrino Fernandes

Publication Activity (10 Years)

Years Active: 2003-2024
Publications (10 Years): 10

Top Topics

Protein Sequences

Molecular Dynamics

Sequence Analysis

Top Venues

J. Chem. Inf. Model.

J. Comput. Chem.

J. Comput. Aided Mol. Des.

Publications

Pedro Ferreira, Rui P. P. Neves, Filipa P. Miranda, Ana V. Cunha, Remco W. A. Havenith, Maria João Ramos, Pedro Alexandrino Fernandes
-Hydroperoxyl Formation. J. Chem. Inf. Model. 64 (10) (2024)
João T. S. Coimbra, Pedro Alexandrino Fernandes, Maria João Ramos
Deciphering the Catalytic Mechanism of Virginiamycin B Lyase with Multiscale Methods and Molecular Dynamics Simulations. J. Chem. Inf. Model. 63 (20) (2023)
Juliana Castro-Amorim, Ana Oliveira, Ashis K. Mukherjee, Maria João Ramos, Pedro Alexandrino Fernandes
Unraveling the Reaction Mechanism of Russell's Viper Venom Factor X Activator: A Paradigm for the Reactivity of Zinc Metalloproteinases? J. Chem. Inf. Model. 63 (13) (2023)
Rui P. P. Neves, Maria João Ramos, Pedro Alexandrino Fernandes
Engineering DszC Mutants from Transition State Macrodipole Considerations and Evolutionary Sequence Analysis. J. Chem. Inf. Model. 63 (1) (2023)
Luís M. C. Teixeira, João T. S. Coimbra, Maria João Ramos, Pedro Alexandrino Fernandes
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. J. Chem. Inf. Model. 62 (10) (2022)
Rui P. P. Neves, Pedro Alexandrino Fernandes, Maria João Ramos
Role of Enzyme and Active Site Conformational Dynamics in the Catalysis by α-Amylase Explored with QM/MM Molecular Dynamics. J. Chem. Inf. Model. 62 (15) (2022)
Pedro Paiva, Maria João Ramos, Pedro Alexandrino Fernandes
Assessing the validity of DLPNO-CCSD(T) in the calculation of activation and reaction energies of ubiquitous enzymatic reactions. J. Comput. Chem. 41 (29) (2020)
Kenneth Goossens, Rui Pp Neves, Pedro Alexandrino Fernandes, Hans De Winter
A Computational and Modeling Study of the Reaction Mechanism of Staphylococcus aureus Monoglycosyltransferase Reveals New Insights on the GT51 Family of Enzymes. J. Chem. Inf. Model. 60 (11) (2020)
Inês C. M. Simões, Inês P. D. Costa, João T. S. Coimbra, Maria João Ramos, Pedro Alexandrino Fernandes
New Parameters for Higher Accuracy in the Computation of Binding Free Energy Differences upon Alanine Scanning Mutagenesis on Protein-Protein Interfaces. J. Chem. Inf. Model. 57 (1) (2017)
Diogo Santos-Martins, Pedro Alexandrino Fernandes, Maria João Ramos
Calculation of distribution coefficients in the SAMPL5 challenge from atomic solvation parameters and surface areas. J. Comput. Aided Mol. Des. 30 (11) (2016)
Diogo Santos, Pedro Alexandrino Fernandes, Henrique Lopes Cardoso, Eugénio C. Oliveira
A Weighted Constraint Optimization Approach to the Nurse Scheduling Problem. CSE (2015)
Sérgio Filipe Sousa, Gaspar R. P. Pinto, António J. M. Ribeiro, João T. S. Coimbra, Pedro Alexandrino Fernandes, Maria João Ramos
Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for copper complexes. J. Comput. Chem. 34 (24) (2013)
Irina S. Moreira, Pedro Alexandrino Fernandes, Maria João Ramos
Protein-protein docking dealing with the unknown. J. Comput. Chem. 31 (2) (2010)
Alexandra T. P. Carvalho, Pedro Alexandrino Fernandes, Marcel Swart, Joost N. P. Van Stralen, F. Matthias Bickelhaupt, Maria João Ramos
Role of the variable active site residues in the function of thioredoxin family oxidoreductases. J. Comput. Chem. 30 (5) (2009)
Sérgio Filipe Sousa, Emanuela S. Carvalho, Diana M. Ferreira, Isabel S. Tavares, Pedro Alexandrino Fernandes, Maria João Ramos, José A. N. F. Gomes
Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for zinc complexes. J. Comput. Chem. 30 (16) (2009)
Natércia F. Brás, Sara A. Moura-Tamames, Pedro Alexandrino Fernandes, Maria João Ramos
Mechanistic studies on the formation of glycosidase-substrate and glycosidase-inhibitor covalent intermediates. J. Comput. Chem. 29 (15) (2008)
Irina S. Moreira, Pedro Alexandrino Fernandes, Maria João Ramos
Computational alanine scanning mutagenesis - An improved methodological approach. J. Comput. Chem. 28 (3) (2007)
Sérgio Filipe Sousa, Pedro Alexandrino Fernandes, Maria João Ramos
Theoretical studies on farnesyl transferase: Evidence for thioether product coordination to the active-site zinc sphere. J. Comput. Chem. 28 (7) (2007)
Alexandra T. P. Carvalho, Pedro Alexandrino Fernandes, Maria João Ramos
Determination of the pKa between the active site cysteines of thioredoxin and DsbA. J. Comput. Chem. 27 (8) (2006)
Nuno M. F. S. A. Cerqueira, Pedro Alexandrino Fernandes, Leif A. Eriksson, Maria João Ramos
Ribonucleotide activation by enzyme ribonucleotide reductase: Understanding the role of the enzyme. J. Comput. Chem. 25 (16) (2004)
Susana Pereira, Pedro Alexandrino Fernandes, Maria João Ramos
Theoretical study of ribonucleotide reductase mechanism-based inhibition by 2-azido-2-deoxyribonucleoside 5-diphosphates. J. Comput. Chem. 25 (2) (2004)
Susana Pereira, Pedro Alexandrino Fernandes, Maria João Ramos
Mechanism for ribonucleotide reductase inactivation by the anticancer drug gemcitabine. J. Comput. Chem. 25 (10) (2004)
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, H. A. Santos, H. D. G. Mangericão, H. M. Martins, H. D. B. Pinto, Hugo R. R. Santos, Irina S. Moreira, M. J. V. Azeredo, R. P. S. Abreu, R. M. S. Oliveira, Sergio F. Sousa, R. J. A. M. Silva, Z. S. Mourão, Maria João Ramos
New designs for MRI contrast agents. J. Comput. Aided Mol. Des. 17 (7) (2003)