João PGLM Rodrigues

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Coauteurs

Alexandre M.J.J. BonvinUtrecht universityAdresse e-mail validée de uu.nl
Panagiotis KastritisProfessor of Integrative Structural Biochemistry, MLU Halle / ERA Chair for cryo-EM, NHRF, AthensAdresse e-mail validée de bct.uni-halle.de
Ezgi KaracaAssistant Professor, Izmir Biomedicine and Genome Center & DEUAdresse e-mail validée de ibg.edu.tr
Mikael TrelletFluigentAdresse e-mail validée de fluigent.com
Adrien MelquiondUniversity Medical Center Utrecht, NLAdresse e-mail validée de umcutrecht.nl
Gydo Van ZundertSchrodingerAdresse e-mail validée de schrodinger.com
Marc van DijkSenior scientist, Vrije Universiteit AmsterdamAdresse e-mail validée de vu.nl
Sjoerd de VriesResearch Engineer, CMPLI, ParisAdresse e-mail validée de inserm.fr
Li C XueRadboud University Medical CenterAdresse e-mail validée de radboudumc.nl
Anna VangoneLarge Molecule Research - RocheAdresse e-mail validée de uu.nl
Michael LevittStructural Biology, Stanford UniversityAdresse e-mail validée de stanford.edu
João M. C. TeixeiraZymvol BiomodelingAdresse e-mail validée de zymvol.com
Cunliang GengNetherlands eScience CenterAdresse e-mail validée de esciencecenter.nl
Ron DrorStanford UniversityAdresse e-mail validée de stanford.edu
Koen M VisscherVrije Universiteit AmsterdamAdresse e-mail validée de vu.nl
Chris SanderHarvard Medical School, Broad Institute, MGH, Dana-Farber Cancer Institute, Memorial Sloan KetteringAdresse e-mail validée de sanderlab.org
Zeynep KurkcuogluPhD Bogazici University, PostDoc Utrecht UniversityAdresse e-mail validée de boun.edu.tr
Rolf BoelensUtrecht UniversityAdresse e-mail validée de uu.nl
Markus WeingarthAssociate Professor for Biomedical NMR, Utrecht UniversityAdresse e-mail validée de uu.nl
Siddarth NarasimhanScientist at WaveBreak TherapeuticsAdresse e-mail validée de wavebreaktx.com

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João PGLM Rodrigues

Principal Scientist, Schrodinger Inc

Adresse e-mail validée de schrodinger.com - Page d'accueil

Computational Biology Structural Biology Biophysics


Titre Trier par citations Trier par année Trier par titre	Citée par Citée par	Année
The HADDOCK2. 2 web server: user-friendly integrative modeling of biomolecular complexes GCP Van Zundert, J Rodrigues, M Trellet, C Schmitz, PL Kastritis, ... Journal of molecular biology 428 (4), 720-725, 2016	2703	2016
PRODIGY: a web server for predicting the binding affinity of protein–protein complexes LC Xue, JP Rodrigues, PL Kastritis, AM Bonvin, A Vangone Bioinformatics 32 (23), 3676-3678, 2016	1099	2016
Sequence co-evolution gives 3D contacts and structures of protein complexes TA Hopf, CPI Schärfe, JP Rodrigues, AG Green, O Kohlbacher, C Sander, ... elife 3, e03430, 2014	545	2014
Structural insights into binding specificity, efficacy and bias of a β₂AR partial agonist M Masureel, Y Zou, LP Picard, E van der Westhuizen, JP Mahoney, ... Nature chemical biology 14 (11), 1059-1066, 2018	196	2018
KoBaMIN: a knowledge-based minimization web server for protein structure refinement JP Rodrigues, M Levitt, G Chopra Nucleic acids research 40 (W1), W323-W328, 2012	170	2012
Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: a CASP‐CAPRI experiment MF Lensink, S Velankar, A Kryshtafovych, SY Huang, ... Proteins: Structure, Function, and Bioinformatics 84, 323-348, 2016	169	2016
Structural and functional analysis of a β2-adrenergic receptor complex with GRK5 KE Komolov, Y Du, NM Duc, RM Betz, JP Rodrigues, RD Leib, D Patra, ... Cell 169 (3), 407-421. e16, 2017	165	2017
Proteins feel more than they see: fine-tuning of binding affinity by properties of the non-interacting surface PL Kastritis, JP Rodrigues, GE Folkers, R Boelens, AMJJ Bonvin Journal of molecular biology 426 (14), 2632-2652, 2014	137	2014
Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predictor in the D3R Grand Challenge 2 Z Kurkcuoglu, PI Koukos, N Citro, ME Trellet, J Rodrigues, IS Moreira, ... Journal of computer-aided molecular design 32, 175-185, 2018	130	2018
Integrative computational modeling of protein interactions JP Rodrigues, AMJJ Bonvin The FEBS journal 281 (8), 1988-2003, 2014	128	2014
Clustering biomolecular complexes by residue contacts similarity JP Rodrigues, M Trellet, C Schmitz, P Kastritis, E Karaca, ASJ Melquiond, ... Proteins: Structure, Function, and Bioinformatics 80 (7), 1810-1817, 2012	128	2012
Community‐wide evaluation of methods for predicting the effect of mutations on protein–protein interactions R Moretti, SJ Fleishman, R Agius, M Torchala, PA Bates, PL Kastritis, ... Proteins: Structure, Function, and Bioinformatics 81 (11), 1980-1987, 2013	115	2013
Predicting the zoonotic capacity of mammals to transmit SARS-CoV-2 IR Fischhoff, AA Castellanos, JP Rodrigues, A Varsani, BA Han Proceedings of the Royal Society B 288 (1963), 20211651, 2021	106	2021
OpenMM 8: molecular dynamics simulation with machine learning potentials P Eastman, R Galvelis, RP Peláez, CRA Abreu, SE Farr, E Gallicchio, ... The Journal of Physical Chemistry B 128 (1), 109-116, 2023	96	2023
Pdb-tools: a swiss army knife for molecular structures JP Rodrigues, JMC Teixeira, M Trellet, AMJJ Bonvin F1000Research 7, 2018	94	2018
Defining the limits of homology modeling in information‐driven protein docking J Rodrigues, ASJ Melquiond, E Karaca, M Trellet, M Van Dijk, ... Proteins: Structure, Function, and Bioinformatics 81 (12), 2119-2128, 2013	78	2013
The supramolecular organization of a peptide-based nanocarrier at high molecular detail M Rad-Malekshahi, KM Visscher, JP Rodrigues, R De Vries, WE Hennink, ... Journal of the American Chemical Society 137 (24), 7775-7784, 2015	77	2015
Insights on cross-species transmission of SARS-CoV-2 from structural modeling JP Rodrigues, S Barrera-Vilarmau, J Mc Teixeira, M Sorokina, E Seckel, ... PLoS computational biology 16 (12), e1008449, 2020	70	2020
Sense and simplicity in HADDOCK scoring: Lessons from CASP‐CAPRI round 1 A Vangone, J Rodrigues, LC Xue, GCP Van Zundert, C Geng, ... Proteins: Structure, Function, and Bioinformatics 85 (3), 417-423, 2017	63	2017
Concept-based query expansion for retrieving gene related publications from MEDLINE S Matos, JP Arrais, J Maia-Rodrigues, JL Oliveira BMC bioinformatics 11, 1-9, 2010	62	2010

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