| 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 | 2703 | 2016 |
| Posttranslational modification of pili upon cell contact triggers N. meningitidis dissemination J Chamot-Rooke, G Mikaty, C Malosse, M Soyer, A Dumont, J Gault, ... Science 331 (6018), 778, 2011 | 220 | 2011 |
| A unified conformational selection and induced fit approach to protein-peptide docking M Trellet, ASJ Melquiond, AMJJ Bonvin PloS one 8 (3), e58769, 2013 | 196 | 2013 |
| Large-scale prediction of binding affinity in protein–small ligand complexes: The PRODIGY-LIG web server A Vangone, J Schaarschmidt, P Koukos, C Geng, N Citro, ME Trellet, ... Bioinformatics 35 (9), 1585-1587, 2019 | 194 | 2019 |
| 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 | 130 | 2018 |
| Blind prediction of homo‐and hetero‐protein complexes: The CASP13‐CAPRI experiment MF Lensink, G Brysbaert, N Nadzirin, S Velankar, RAG Chaleil, T Gerguri, ... Proteins: Structure, Function, and Bioinformatics 87 (12), 1200-1221, 2019 | 128 | 2019 |
| 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 | 128 | 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 | 115 | 2013 |
| SpotOn: high accuracy identification of protein-protein interface hot-spots IS Moreira, PI Koukos, R Melo, JG Almeida, AJ Preto, J Schaarschmidt, ... Scientific reports 7 (1), 8007, 2017 | 96 | 2017 |
| Pdb-tools: a swiss army knife for molecular structures JP Rodrigues, JMC Teixeira, M Trellet, AMJJ Bonvin F1000Research 7, 2018 | 94 | 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 | 78 | 2013 |
| 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 | 64 | 2017 |
| The HADDOCK2. 4 web server for integrative modeling of biomolecular complexes RV Honorato, ME Trellet, B Jiménez-García, JJ Schaarschmidt, M Giulini, ... Nature Protocols, 1-23, 2024 | 60 | 2024 |
| The DisVis and PowerFit web servers: explorative and integrative modeling of biomolecular complexes GCP Van Zundert, M Trellet, J Schaarschmidt, Z Kurkcuoglu, M David, ... Journal of molecular biology 429 (3), 399-407, 2017 | 58 | 2017 |
| Inhibition of the integrated stress response by viral proteins that block p-eIF2–eIF2B association HH Rabouw, LJ Visser, TC Passchier, MA Langereis, F Liu, P Giansanti, ... Nature Microbiology 5 (11), 1361-1373, 2020 | 46 | 2020 |
| Sharing data from molecular simulations M Abraham, R Apostolov, J Barnoud, P Bauer, C Blau, AMJJ Bonvin, ... Journal of chemical information and modeling 59 (10), 4093-4099, 2019 | 39 | 2019 |
| Semantics for an integrative and immersive pipeline combining visualization and analysis of molecular data M Trellet, N Férey, J Flotyński, M Baaden, P Bourdot Journal of integrative bioinformatics 15 (2), 20180004, 2018 | 29 | 2018 |
| PDB‐tools Web: A User‐friendly Interface for the Manipulation of PDB Files B Jiménez‐García, JMC Teixeira, M Trellet, JP Rodrigues, AMJJ Bonvin Proteins: Structure, Function, and Bioinformatics 89 (3), 330-335, 2021 | 25 | 2021 |
| Folding then binding vs folding through binding in macrocyclic peptide inhibitors of human pancreatic α-amylase L Goldbach, BJA Vermeulen, S Caner, M Liu, C Tysoe, L van Gijzel, ... ACS chemical biology 14 (8), 1751-1759, 2019 | 25 | 2019 |
| Information-driven modeling of protein-peptide complexes M Trellet, ASJ Melquiond, AMJJ Bonvin Computational Peptidology, 221-239, 2015 | 24 | 2015 |
Alexandre M.J.J. BonvinUtrecht universityEmail confirmado em uu.nl