| 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 | 1507 | 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 | 510 | 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 | 443 | 2014 |
| 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 | 155 | 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 | 143 | 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 | 120 | 2017 |
| 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 | 119 | 2018 |
| Integrative computational modeling of protein interactions JP Rodrigues, AMJJ Bonvin The FEBS journal 281 (8), 1988-2003, 2014 | 114 | 2014 |
| 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 | 100 | 2014 |
| 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 | 100 | 2013 |
| 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 | 99 | 2012 |
| 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 | 73 | 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 | 65 | 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 | 64 | 2015 |
| 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 | 55 | 2010 |
| 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 | 50 | 2010 |
| 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 | 45 | 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 | 37 | 2017 |
| 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 | 33 | 2017 |
| 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 | 33 | 2014 |
Alexandre M.J.J. BonvinUtrecht universityVerified email at uu.nl
