Joćo PGLM Rodrigues
Joćo PGLM Rodrigues
Postdoctoral Researcher (Levitt Lab), Stanford University
Geverifieerd e-mailadres voor stanford.edu - Homepage
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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
7522016
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
3192014
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
1732016
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
1432012
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
1062016
Integrative computational modeling of protein interactions
JP Rodrigues, AMJJ Bonvin
The FEBS journal 281 (8), 1988-2003, 2014
952014
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
922013
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
832017
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
692012
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
662014
Concept-based query expansion for retrieving gene related publications from MEDLINE
S Matos, JP Arrais, J Maia-Rodrigues, JL Oliveira
BMC bioinformatics 11 (1), 212, 2010
522010
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
512013
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
502015
Structural insights into binding specificity, efficacy and bias of a β 2 AR partial agonist
M Masureel, Y Zou, LP Picard, E van der Westhuizen, JP Mahoney, ...
Nature chemical biology 14 (11), 1059-1066, 2018
472018
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
452010
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
272018
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
232017
Supramolecular Organization and Functional Implications of K+ Channel Clusters in Membranes
KM Visscher, J Medeiros‐Silva, D Mance, JP Rodrigues, M Daniėls, ...
Angewandte Chemie International Edition 56 (43), 13222-13227, 2017
202017
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
202014
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
192017
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Artikelen 1–20