Updates to the integrated protein–protein interaction benchmarks: docking benchmark version 5 and affinity benchmark version 2 T Vreven, IH Moal, A Vangone, BG Pierce, PL Kastritis, M Torchala, ... Journal of molecular biology 427 (19), 3031-3041, 2015 | 433 | 2015 |
Structural biology in the clouds: the WeNMR-EOSC ecosystem RV Honorato, PI Koukos, B Jiménez-García, A Tsaregorodtsev, M Verlato, ... Frontiers in molecular biosciences 8, 729513, 2021 | 391 | 2021 |
pyDockWEB: a web server for rigid-body protein–protein docking using electrostatics and desolvation scoring B Jiménez-García, C Pons, J Fernández-Recio Bioinformatics 29 (13), 1698-1699, 2013 | 272 | 2013 |
SKEMPI 2.0: an updated benchmark of changes in protein–protein binding energy, kinetics and thermodynamics upon mutation J Jankauskaitė, B Jiménez-García, J Dapkūnas, J Fernández-Recio, ... Bioinformatics 35 (3), 462-469, 2019 | 251 | 2019 |
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 | 166 | 2016 |
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 | 117 | 2019 |
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 | 113 | 2013 |
LightDock: a new multi-scale approach to protein–protein docking B Jiménez-García, J Roel-Touris, M Romero-Durana, M Vidal, ... Bioinformatics 34 (1), 49-55, 2018 | 88 | 2018 |
Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment MF Lensink, G Brysbaert, T Mauri, N Nadzirin, S Velankar, RAG Chaleil, ... Proteins: Structure, Function, and Bioinformatics 89 (12), 1800-1823, 2021 | 85 | 2021 |
Modeling antibody-antigen complexes by information-driven docking F Ambrosetti, B Jiménez-García, J Roel-Touris, AMJJ Bonvin Structure 28 (1), 119-129. e2, 2020 | 74 | 2020 |
pyDockSAXS: protein–protein complex structure by SAXS and computational docking B Jiménez-García, C Pons, DI Svergun, P Bernadó, J Fernández-Recio Nucleic acids research 43 (W1), W356-W361, 2015 | 72 | 2015 |
CCharPPI web server: computational characterization of protein–protein interactions from structure IH Moal, B Jiménez-García, J Fernández-Recio Bioinformatics 31 (1), 123-125, 2015 | 70 | 2015 |
Blind prediction of interfacial water positions in CAPRI MF Lensink, IH Moal, PA Bates, PL Kastritis, ASJ Melquiond, E Karaca, ... Proteins: Structure, Function, and Bioinformatics 82 (4), 620-632, 2014 | 61 | 2014 |
A protein‐RNA docking benchmark (II): Extended set from experimental and homology modeling data L Pérez‐Cano, B Jiménez‐García, J Fernández‐Recio Proteins: Structure, Function, and Bioinformatics 80 (7), 1872-1882, 2012 | 60 | 2012 |
IRaPPA: information retrieval based integration of biophysical models for protein assembly selection IH Moal, D Barradas-Bautista, B Jiménez-García, M Torchala, ... Bioinformatics 33 (12), 1806-1813, 2017 | 38 | 2017 |
proABC-2: PRediction of AntiBody contacts v2 and its application to information-driven docking F Ambrosetti, TH Olsen, PP Olimpieri, B Jiménez-García, E Milanetti, ... Bioinformatics 36 (20), 5107-5108, 2020 | 37 | 2020 |
Integrative modeling of membrane-associated protein assemblies J Roel-Touris, B Jiménez-García, AMJJ Bonvin Nature communications 11 (1), 6210, 2020 | 30 | 2020 |
LightDock goes information-driven J Roel-Touris, AMJJ Bonvin, B Jiménez-García Bioinformatics 36 (3), 950-952, 2020 | 30 | 2020 |
PRODIGY-crystal: a web-tool for classification of biological interfaces in protein complexes B Jiménez-García, K Elez, PI Koukos, AM Bonvin, A Vangone Bioinformatics 35 (22), 4821-4823, 2019 | 29 | 2019 |
Expanding the frontiers of protein–protein modeling: from docking and scoring to binding affinity predictions and other challenges C Pallara, B Jiménez‐García, L Pérez‐Cano, M Romero‐Durana, ... Proteins: Structure, Function, and Bioinformatics 81 (12), 2192-2200, 2013 | 26 | 2013 |