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ORCIDPedro Alexandrino Fernandes
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Journal Articles
- 2024
[j22]Pedro Ferreira
, Rui P. P. Neves, Filipa P. Miranda, Ana V. Cunha, Remco W. A. Havenith, Maria João Ramos, Pedro Alexandrino Fernandes:
DszA Catalyzes C-S Bond Cleavage through N5-Hydroperoxyl Formation. J. Chem. Inf. Model. 64(10): 4218-4230 (2024)- 2023
- [j21]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): 20-26 (2023) - [j20]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): 4056-4069 (2023) - [j19]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): 6354-6365 (2023) - 2022
- [j18]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): 2510-2521 (2022) - [j17]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): 3638-3650 (2022) - 2020
- [j16]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): 2459-2468 (2020) - [j15]Kenneth Goossens, Rui P. P. 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): 5513-5528 (2020) - 2017
- [j14]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): 60-72 (2017) - 2016
- [j13]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): 1079-1086 (2016) - 2013
- [j12]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): 2079-2090 (2013) - 2010
- [j11]Irina S. Moreira, Pedro Alexandrino Fernandes, Maria João Ramos:
Protein-protein docking dealing with the unknown. J. Comput. Chem. 31(2): 317-342 (2010) - 2009
- [j10]Alexandra T. P. Carvalho, Pedro Alexandrino Fernandes, Marcel Swart, Joost N. P. Van Stralen, Friedrich Matthias Bickelhaupt, Maria João Ramos:
Role of the variable active site residues in the function of thioredoxin family oxidoreductases. J. Comput. Chem. 30(5): 710-724 (2009) - [j9]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): 2752-2763 (2009) - 2008
- [j8]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): 2565-2574 (2008) - 2007
- [j7]Irina S. Moreira, Pedro Alexandrino Fernandes, Maria João Ramos:
Computational alanine scanning mutagenesis - An improved methodological approach. J. Comput. Chem. 28(3): 644-654 (2007) - [j6]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): 1160-1168 (2007) - 2006
- [j5]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): 966-975 (2006) - 2004
- [j4]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): 227-237 (2004) - [j3]Susana Pereira, Pedro Alexandrino Fernandes, Maria João Ramos:
Mechanism for ribonucleotide reductase inactivation by the anticancer drug gemcitabine. J. Comput. Chem. 25(10): 1286-1294 (2004) - [j2]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): 2031-2037 (2004) - 2003
- [j1]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, 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): 463-473 (2003)
Conference and Workshop Papers
- 2015
- [c1]Diogo Santos, Pedro Alexandrino Fernandes, Henrique Lopes Cardoso, Eugénio C. Oliveira:
A Weighted Constraint Optimization Approach to the Nurse Scheduling Problem. CSE 2015: 233-239
Coauthor Index
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