עקוב אחר
João PGLM Rodrigues
João PGLM Rodrigues
Principal Scientist, Schrodinger Inc
כתובת אימייל מאומתת בדומיין schrodinger.com - דף הבית
כותרת
צוטט על ידי
צוטט על ידי
שנה
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
27412016
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
11322016
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
5582014
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
1972018
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
1722012
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
1692016
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
1642017
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
1382014
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
1322018
Integrative computational modeling of protein interactions‏
JP Rodrigues, AMJJ Bonvin‏
The FEBS journal 281 (8), 1988-2003, 2014‏
1292014
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
1272012
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
1142013
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
1062023
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
1062021
pdb-tools: A swiss army knife for molecular structures‏
JP Rodrigues, JMC Teixeira, M Trellet, AMJJ Bonvin‏
F1000Research 7, 1961, 2018‏
1032018
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
792015
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
782013
The HADDOCK2. 4 web server for integrative modeling of biomolecular complexes‏
RV Honorato, ME Trellet, B Jiménez-García, JJ Schaarschmidt, M Giulini, ...‏
Nature protocols 19 (11), 3219-3241, 2024‏
712024
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
682020
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
642010
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מאמרים 1–20