| 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 | 2749 | 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 | 1133 | 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 | 557 | 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 | 197 | 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 | 172 | 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 | 168 | 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 | 164 | 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 | 138 | 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 | 133 | 2018 |
| Integrative computational modeling of protein interactions JP Rodrigues, AMJJ Bonvin The FEBS journal 281 (8), 1988-2003, 2014 | 129 | 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 | 127 | 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 | 114 | 2013 |
| OpenMM 8: molecular dynamics simulation with machine learning potentials P Eastman, R Galvelis, RP Pelįez, CRA Abreu, SE Farr, E Gallicchio, ... The Journal of Physical Chemistry B 128 (1), 109-116, 2023 | 110 | 2023 |
| 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 |
| pdb-tools: A swiss army knife for molecular structures JP Rodrigues, JMC Teixeira, M Trellet, AMJJ Bonvin F1000Research 7, 1961, 2018 | 103 | 2018 |
| 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 | 79 | 2015 |
| 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 HADDOCK2. 4 web server for integrative modeling of biomolecular complexes RV Honorato, ME Trellet, B Jiménez-Garcķa, JJ Schaarschmidt, M Giulini, ... Nature protocols 19 (11), 3219-3241, 2024 | 74 | 2024 |
| 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 | 68 | 2020 |
| 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 | 64 | 2010 |
Alexandre M.J.J. BonvinUtrecht universityVerified email at uu.nl
