Maria João Ramos

Publication Activity (10 Years)

Years Active: 1997-2024
Publications (10 Years): 10

Top Topics

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)
Henrique S. Fernandes, Maria João Ramos, Nuno M. F. S. A. Cerqueira
molUP: A VMD plugin to handle QM and ONIOM calculations using the gaussian software. J. Comput. Chem. 39 (19) (2018)
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-Martins, Stefano Forli, Maria João Ramos, Arthur J. Olson
: An Improved AutoDock Force Field for Small-Molecule Docking to Zinc Metalloproteins. J. Chem. Inf. Model. 54 (8) (2014)
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)
Alexandra T. P. Carvalho, Ana F. S. Teixeira, Maria João Ramos
Parameters for molecular dynamics simulations of iron-sulfur proteins. J. Comput. Chem. 34 (18) (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)
Hugo R. R. Santos, Gregori Ujaque, Maria João Ramos, José A. N. F. Gomes
QM/QM study of the coverage effects on the adsorption of amino-cyclopentene at the Si(100) surface. J. Comput. Chem. 27 (15) (2006)
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)
César Portela, Carlos M. M. Afonso, Madalena M. M. Pinto, Maria João Ramos
Computational studies of new potential antimalarial compounds - Stereoelectronic complementarity with the receptor. J. Comput. Aided Mol. Des. 17 (9) (2003)
Vineet Pande, Rakesh K. Sharma, Jun-Ichiro Inoue, Masami Otsuka, Maria João Ramos
A molecular modeling study of inhibitors of nuclear factor kappa-B (p50) - DNA binding. J. Comput. Aided Mol. Des. 17 (12) (2003)
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)
Elsa S. Henriques, Wely B. Floriano, Nathalie Reuter, André Melo, David Brown, José A. N. F. Gomes, Bernard Maigret, Marco A. C. Nascimento, Maria João Ramos
The search for a new model structure of beta-Factor XIIa. J. Comput. Aided Mol. Des. 15 (4) (2001)
André Melo, André T. Puga, Fernanda Gentil, Nelson Brito, Artur Pimenta Alves, Maria João Ramos
Byte Structure Variable Length Coding (BS-VLC): A New Specific Algorithm Applied in the Compression of Trajectories Generated by Molecular Dynamics. J. Chem. Inf. Comput. Sci. 40 (3) (2000)
Elsa F. Henriques, Maria João Ramos, Christopher A. Reynolds
Inclusion of conserved buried water molecules in the model structure of rat submaxillary kallikrein. J. Comput. Aided Mol. Des. 12 (6) (1998)
Elsa F. Henriques, Maria João Ramos, Christopher A. Reynolds
Inclusion of conserved buried water molecules in the model structure of rat submaxillary kallikrein. J. Comput. Aided Mol. Des. 11 (6) (1997)