João P. G. L. M. Rodrigues

According to our database, João P. G. L. M. Rodrigues authored at least 8 papers between 2012 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2023

OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials.

Peter K. Eastman, Raimondas Galvelis, Raúl P. Peláez, Charlles R. A. Abreu, Stephen E. Farr, Emilio Gallicchio, Anton Gorenko, Michael M. Henry, Frank Hu, Jing Huang, Andreas Krämer, Julien Michel, Joshua A. Mitchell, Vijay S. Pande, João P. G. L. M. Rodrigues, Jaime Rodríguez-Guerra, Andrew C. Simmonett, Jason M. Swails, Ivy Zhang, John D. Chodera, Gianni De Fabritiis, Thomas E. Markland

CoRR, 2023

2020

Insights on cross-species transmission of SARS-CoV-2 from structural modeling.

João P. G. L. M. Rodrigues, Susana Barrera-Vilarmau, João M. C. Teixeira, Marija Sorokina, Elizabeth Seckel, Panagiotis L. Kastritis, Michael Levitt

PLoS Comput. Biol., 2020

2018

Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2.

Zeynep Kurkcuoglu, Panagiotis I. Koukos, Nevia Citro, Mikael E. Trellet, João P. G. L. M. Rodrigues, Irina S. Moreira, Jorge Roel-Touris, Adrien S. J. Melquiond, Cunliang Geng, Jörg Schaarschmidt, Li C. Xue, Anna Vangone, Alexandre M. J. J. Bonvin

J. Comput. Aided Mol. Des., 2018

pdb-tools: a swiss army knife for molecular structures.

João P. G. L. M. Rodrigues, João M. C. Teixeira, Mikaël Trellet, Alexandre M. J. J. Bonvin

F1000Research, 2018

2017

Template-based protein-protein docking exploiting pairwise interfacial residue restraints.

Li C. Xue, João P. G. L. M. Rodrigues, Drena Dobbs, Vasant G. Honavar, Alexandre M. J. J. Bonvin

Briefings Bioinform., 2017

2016

PRODIGY: a web server for predicting the binding affinity of protein-protein complexes.

Li C. Xue, João P. G. L. M. Rodrigues, Panagiotis L. Kastritis, Alexandre M. J. J. Bonvin, Anna Vangone

Bioinform., 2016

2014

HADDOCK_2P2I: A Biophysical Model for Predicting the Binding Affinity of Protein-Protein Interaction Inhibitors.

Panagiotis L. Kastritis, João P. G. L. M. Rodrigues, Alexandre M. J. J. Bonvin

J. Chem. Inf. Model., 2014

2012

KoBaMIN: a knowledge-based minimization web server for protein structure refinement.

João P. G. L. M. Rodrigues, Michael Levitt, Gaurav Chopra

Nucleic Acids Res., 2012