João P. G. L. M. Rodrigues

Publication Activity (10 Years)

Years Active: 2012-2023
Publications (10 Years): 6

Top Topics

Grand Challenge

Protein Complexes

Computational Methods

Top Venues

Briefings Bioinform.

J. Chem. Inf. Model.

Publications

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
OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. CoRR (2023)
João P. G. L. M. Rodrigues, Susana Barrera-Vilarmau, João M. C. Teixeira, Marija Sorokina, Elizabeth Seckel, Panagiotis L. Kastritis, Michael Levitt
Insights on cross-species transmission of SARS-CoV-2 from structural modeling. PLoS Comput. Biol. 16 (12) (2020)
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
Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2. J. Comput. Aided Mol. Des. 32 (1) (2018)
João P. G. L. M. Rodrigues, João M. C. Teixeira, Mikaël Trellet, Alexandre M. J. J. Bonvin
pdb-tools: a swiss army knife for molecular structures. F1000Research 7 (2018)
Li C. Xue, João P. G. L. M. Rodrigues, Drena Dobbs, Vasant G. Honavar, Alexandre M. J. J. Bonvin
Template-based protein-protein docking exploiting pairwise interfacial residue restraints. Briefings Bioinform. 18 (3) (2017)
Li C. Xue, João P. G. L. M. Rodrigues, Panagiotis L. Kastritis, Alexandre M. J. J. Bonvin, Anna Vangone
PRODIGY: a web server for predicting the binding affinity of protein-protein complexes. Bioinform. 32 (23) (2016)
Panagiotis L. Kastritis, João P. G. L. M. Rodrigues, Alexandre M. J. J. Bonvin
: A Biophysical Model for Predicting the Binding Affinity of Protein-Protein Interaction Inhibitors. J. Chem. Inf. Model. 54 (3) (2014)
João P. G. L. M. Rodrigues, Michael Levitt, Gaurav Chopra
KoBaMIN: a knowledge-based minimization web server for protein structure refinement. Nucleic Acids Res. 40 (Web-Server-Issue) (2012)