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Joćo PGLM Rodrigues
Joćo PGLM Rodrigues
Senior Scientist, Schrodinger Inc
Verified email at schrodinger.com - Homepage
Title
Cited by
Cited by
Year
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
15072016
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
5102016
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
4432014
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
1552012
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
1432016
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
1202017
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
1192018
Integrative computational modeling of protein interactions
JP Rodrigues, AMJJ Bonvin
The FEBS journal 281 (8), 1988-2003, 2014
1142014
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
1002014
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
1002013
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
992012
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 (1), 175-185, 2018
732018
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
652013
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
642015
Concept-based query expansion for retrieving gene related publications from MEDLINE
S Matos, JP Arrais, J Maia-Rodrigues, JL Oliveira
BMC bioinformatics 11 (1), 1-9, 2010
552010
Strengths and weaknesses of data‐driven docking in critical assessment of prediction of interactions
SJ de Vries, ASJ Melquiond, PL Kastritis, E Karaca, A Bordogna, ...
Proteins: Structure, Function, and Bioinformatics 78 (15), 3242-3249, 2010
502010
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
452020
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
372017
M3: an integrative framework for structure determination of molecular machines
E Karaca, JP Rodrigues, A Graziadei, AMJJ Bonvin, T Carlomagno
Nature methods 14 (9), 897-902, 2017
332017
HADDOCK2P2I: A Biophysical Model for Predicting the Binding Affinity of Protein–Protein Interaction Inhibitors
PL Kastritis, JP Rodrigues, AMJJ Bonvin
Journal of chemical information and modeling 54 (3), 826-836, 2014
332014
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