| 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 | 1404 | 2016 |
| Contacts-based prediction of binding affinity in protein–protein complexes A Vangone, AMJJ Bonvin elife 4, e07454, 2015 | 667 | 2015 |
| 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 | 515 | 2015 |
| COCOMAPS: a web application to analyze and visualize contacts at the interface of biomolecular complexes A Vangone, R Spinelli, V Scarano, L Cavallo, R Oliva Bioinformatics 27 (20), 2915-2916, 2011 | 308 | 2011 |
| 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 | 257 | 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 | 176 | 2016 |
| 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 | 155 | 2018 |
| PRODIGY: a contact-based predictor of binding affinity in protein-protein complexes A Vangone, AMJJ Bonvin Bio-protocol 7 (3), e2124-e2124, 2017 | 137 | 2017 |
| iSEE: Interface structure, evolution, and energy‐based machine learning predictor of binding affinity changes upon mutations C Geng, A Vangone, GE Folkers, LC Xue, AMJJ Bonvin Proteins: Structure, Function, and Bioinformatics 87 (2), 110-119, 2019 | 101 | 2019 |
| 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 | 77 | 2017 |
| Ranking multiple docking solutions based on the conservation of inter‐residue contacts R Oliva, A Vangone, L Cavallo Proteins: Structure, Function, and Bioinformatics 81 (9), 1571-1584, 2013 | 47 | 2013 |
| 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 | 46 | 2019 |
| CONSRANK: a server for the analysis, comparison and ranking of docking models based on inter-residue contacts E Chermak, A Petta, L Serra, A Vangone, V Scarano, L Cavallo, R Oliva Bioinformatics 31 (9), 1481-1483, 2015 | 45 | 2015 |
| MDcons: Intermolecular contact maps as a tool to analyze the interface of protein complexes from molecular dynamics trajectories S Abdel-Azeim, E Chermak, A Vangone, R Oliva, L Cavallo BMC bioinformatics 15 (Suppl 5), S1, 2014 | 42 | 2014 |
| CONS-COCOMAPS: a novel tool to measure and visualize the conservation of inter-residue contacts in multiple docking solutions A Vangone, R Oliva, L Cavallo Bmc Bioinformatics 13 (Suppl 4), S19, 2012 | 42 | 2012 |
| Distinguishing crystallographic from biological interfaces in protein complexes: role of intermolecular contacts and energetics for classification K Elez, AMJJ Bonvin, A Vangone BMC bioinformatics 19 (Suppl 15), 438, 2018 | 40 | 2018 |
| Exploring the interplay between experimental methods and the performance of predictors of binding affinity change upon mutations in protein complexes C Geng, A Vangone, AMJJ Bonvin Protein Engineering, Design and Selection 29 (8), 291-299, 2016 | 35 | 2016 |
| Using a consensus approach based on the conservation of inter‐residue contacts to rank CAPRI models A Vangone, L Cavallo, R Oliva Proteins: Structure, Function, and Bioinformatics 81 (12), 2210-2220, 2013 | 32 | 2013 |
| Structural basis for mutations of human aquaporins associated to genetic diseases L Calvanese, G D’Auria, A Vangone, L Falcigno, R Oliva International Journal of Molecular Sciences 19 (6), 1577, 2018 | 27 | 2018 |
| D936Y and other mutations in the fusion core of the SARS-CoV-2 spike protein heptad repeat 1: frequency, geographical distribution, and structural effect R Oliva, AR Shaikh, A Petta, A Vangone, L Cavallo Molecules 26 (9), 2622, 2021 | 23 | 2021 |
Alexandre M.J.J. BonvinUtrecht universityVerified email at uu.nl
