Maria João Ramos

32 papers Journal 32

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Mechanism of Polyester Hydrolysis by Marine Bacterium PE-H Enzyme: an Atomistic and Thermodynamic Characterization. J. Chem. Inf. Model. Samah Nassir, Pedro Paiva, Rui P. P. Neves, Pedro Alexandrino Fernandes, Achraf El Allali, Maria João Ramos
2024	J	`jnl`	DszA Catalyzes C-S Bond Cleavage through N J. Chem. Inf. Model. Pedro Ferreira, Rui P. P. Neves, Filipa P. Miranda, Ana V. Cunha, Remco W. A. Havenith, Maria João Ramos, Pedro Alexandrino Fernandes
2023	J	`jnl`	Deciphering the Catalytic Mechanism of Virginiamycin B Lyase with Multiscale Methods and Molecular Dynamics Simulations. J. Chem. Inf. Model. João T. S. Coimbra, Pedro Alexandrino Fernandes, Maria João Ramos
2023	J	`jnl`	Engineering DszC Mutants from Transition State Macrodipole Considerations and Evolutionary Sequence Analysis. J. Chem. Inf. Model. Rui P. P. Neves, Maria João Ramos, Pedro Alexandrino Fernandes
2023	J	`jnl`	Unraveling the Reaction Mechanism of Russell's Viper Venom Factor X Activator: A Paradigm for the Reactivity of Zinc Metalloproteinases? J. Chem. Inf. Model. Juliana Castro-Amorim, Ana Oliveira, Ashis K. Mukherjee, Maria João Ramos, Pedro Alexandrino Fernandes
2022	J	`jnl`	Role of Enzyme and Active Site Conformational Dynamics in the Catalysis by α-Amylase Explored with QM/MM Molecular Dynamics. J. Chem. Inf. Model. Rui P. P. Neves, Pedro Alexandrino Fernandes, Maria João Ramos
2022	J	`jnl`	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. Luís M. C. Teixeira, João T. S. Coimbra, Maria João Ramos, Pedro Alexandrino Fernandes
2020	J	`jnl`	Assessing the validity of DLPNO-CCSD(T) in the calculation of activation and reaction energies of ubiquitous enzymatic reactions. J. Comput. Chem. Pedro Paiva, Maria João Ramos, Pedro Alexandrino Fernandes
2018	J	`jnl`	molUP: A VMD plugin to handle QM and ONIOM calculations using the gaussian software. J. Comput. Chem. Henrique S. Fernandes, Maria João Ramos, Nuno M. F. S. A. Cerqueira
2017	J	`jnl`	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. Inês C. M. Simões, Inês P. D. Costa, João T. S. Coimbra, Maria João Ramos, Pedro Alexandrino Fernandes
2016	J	`jnl`	Calculation of distribution coefficients in the SAMPL5 challenge from atomic solvation parameters and surface areas. J. Comput. Aided Mol. Des. Diogo Santos-Martins, Pedro Alexandrino Fernandes, Maria João Ramos
2014	J	`jnl`	AutoDock4 J. Chem. Inf. Model. Diogo Santos-Martins, Stefano Forli, Maria João Ramos, Arthur J. Olson
2013	J	`jnl`	Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for copper complexes. J. Comput. Chem. Sérgio Filipe Sousa, Gaspar R. P. Pinto, António J. M. Ribeiro, João T. S. Coimbra, Pedro Alexandrino Fernandes, Maria João Ramos
2013	J	`jnl`	Parameters for molecular dynamics simulations of iron-sulfur proteins. J. Comput. Chem. Alexandra T. P. Carvalho, Ana F. S. Teixeira, Maria João Ramos
2010	J	`jnl`	Protein-protein docking dealing with the unknown. J. Comput. Chem. Irina S. Moreira, Pedro Alexandrino Fernandes, Maria João Ramos
2009	J	`jnl`	Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for zinc complexes. J. Comput. Chem. Sérgio Filipe Sousa, Emanuela S. Carvalho, Diana M. Ferreira, Isabel S. Tavares, Pedro Alexandrino Fernandes, Maria João Ramos, José A. N. F. Gomes
2009	J	`jnl`	Role of the variable active site residues in the function of thioredoxin family oxidoreductases. J. Comput. Chem. Alexandra T. P. Carvalho, Pedro Alexandrino Fernandes, Marcel Swart, Joost N. P. Van Stralen, Friedrich Matthias Bickelhaupt, Maria João Ramos
2008	J	`jnl`	Mechanistic studies on the formation of glycosidase-substrate and glycosidase-inhibitor covalent intermediates. J. Comput. Chem. Natércia F. Brás, Sara A. Moura-Tamames, Pedro Alexandrino Fernandes, Maria João Ramos
2007	J	`jnl`	Computational alanine scanning mutagenesis - An improved methodological approach. J. Comput. Chem. Irina S. Moreira, Pedro Alexandrino Fernandes, Maria João Ramos
2007	J	`jnl`	Theoretical studies on farnesyl transferase: Evidence for thioether product coordination to the active-site zinc sphere. J. Comput. Chem. Sérgio Filipe Sousa, Pedro Alexandrino Fernandes, Maria João Ramos
2006	J	`jnl`	Determination of the pKa between the active site cysteines of thioredoxin and DsbA. J. Comput. Chem. Alexandra T. P. Carvalho, Pedro Alexandrino Fernandes, Maria João Ramos
2006	J	`jnl`	QM/QM study of the coverage effects on the adsorption of amino-cyclopentene at the Si(100) surface. J. Comput. Chem. Hugo R. R. Santos, Gregori Ujaque, Maria João Ramos, José A. N. F. Gomes
2004	J	`jnl`	Mechanism for ribonucleotide reductase inactivation by the anticancer drug gemcitabine. J. Comput. Chem. Susana Pereira, Pedro Alexandrino Fernandes, Maria João Ramos
2004	J	`jnl`	Ribonucleotide activation by enzyme ribonucleotide reductase: Understanding the role of the enzyme. J. Comput. Chem. Nuno M. F. S. A. Cerqueira, Pedro Alexandrino Fernandes, Leif A. Eriksson, Maria João Ramos
2004	J	`jnl`	Theoretical study of ribonucleotide reductase mechanism-based inhibition by 2-azido-2-deoxyribonucleoside 5-diphosphates. J. Comput. Chem. Susana Pereira, Pedro Alexandrino Fernandes, Maria João Ramos
2003	J	`jnl`	A molecular modeling study of inhibitors of nuclear factor kappa-B (p50) - DNA binding. J. Comput. Aided Mol. Des. Vineet Pande, Rakesh K. Sharma, Jun-Ichiro Inoue, Masami Otsuka, Maria João Ramos
2003	J	`jnl`	Computational studies of new potential antimalarial compounds - Stereoelectronic complementarity with the receptor. J. Comput. Aided Mol. Des. César Portela, Carlos M. M. Afonso, Madalena M. M. Pinto, Maria João Ramos
2003	J	`jnl`	New designs for MRI contrast agents. J. Comput. Aided Mol. Des. 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
2001	J	`jnl`	The search for a new model structure of beta-Factor XIIa. J. Comput. Aided Mol. Des. 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
2000	J	`jnl`	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. André Melo, André T. Puga, Fernanda Gentil, Nelson Brito, Artur Pimenta Alves, Maria João Ramos
1998	J	`jnl`	Inclusion of conserved buried water molecules in the model structure of rat submaxillary kallikrein. J. Comput. Aided Mol. Des. Elsa F. Henriques, Maria João Ramos, Christopher A. Reynolds
1997	J	`jnl`	Inclusion of conserved buried water molecules in the model structure of rat submaxillary kallikrein. J. Comput. Aided Mol. Des. Elsa F. Henriques, Maria João Ramos, Christopher A. Reynolds