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ORCIDJoão P. G. L. M. Rodrigues
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Journal Articles
- 2020
[j6]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)- 2018
- [j5]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): 175-185 (2018) - 2017
- [j4]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): 458-466 (2017) - 2016
- [j3]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): 3676-3678 (2016) - 2014
- [j2]Panagiotis L. Kastritis, João P. G. L. M. Rodrigues, Alexandre M. J. J. Bonvin:
HADDOCK2P2I: A Biophysical Model for Predicting the Binding Affinity of Protein-Protein Interaction Inhibitors. J. Chem. Inf. Model. 54(3): 826-836 (2014) - 2012
- [j1]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): 323-328 (2012)
Informal and Other Publications
- 2023
- [i2]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 abs/2310.03121 (2023) - 2018
- [i1]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: 1961 (2018)
Coauthor Index
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