| 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 | 1096 | 2016 |
| Computational prediction of protein interfaces: A review of data driven methods LC Xue, D Dobbs, AMJJ Bonvin, V Honavar FEBS letters 589 (23), 3516-3526, 2015 | 203 | 2015 |
| 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 |
| 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 | 169 | 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, 175-185, 2018 | 130 | 2018 |
| DeepRank-GNN: a graph neural network framework to learn patterns in protein–protein interfaces M Réau, N Renaud, LC Xue, AMJJ Bonvin Bioinformatics 39 (1), btac759, 2023 | 129 | 2023 |
| 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 |
| RNABindRPlus: a predictor that combines machine learning and sequence homology-based methods to improve the reliability of predicted RNA-binding residues in proteins RR Walia, LC Xue, K Wilkins, Y El-Manzalawy, D Dobbs, V Honavar PloS one 9 (5), e97725, 2014 | 123 | 2014 |
| HomPPI: a class of sequence homology based protein-protein interface prediction methods LC Xue, D Dobbs, V Honavar BMC bioinformatics 12, 1-24, 2011 | 117 | 2011 |
| Finding the ΔΔG spot: Are predictors of binding affinity changes upon mutations in protein–protein interactions ready for it? C Geng, LC Xue, J Roel‐Touris, AMJJ Bonvin Wiley Interdisciplinary Reviews: Computational Molecular Science 9 (5), e1410, 2019 | 114 | 2019 |
| The simultaneous effect of polymer chemistry and device geometry on the in vitro activation of murine dendritic cells LK Petersen, L Xue, MJ Wannemuehler, K Rajan, B Narasimhan Biomaterials 30 (28), 5131-5142, 2009 | 90 | 2009 |
| DeepRank: a deep learning framework for data mining 3D protein-protein interfaces N Renaud, C Geng, S Georgievska, F Ambrosetti, L Ridder, DF Marzella, ... Nature communications 12 (1), 7068, 2021 | 89 | 2021 |
| 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 | 89 | 2019 |
| Using Fourier spectrum analysis and pseudo amino acid composition for prediction of membrane protein types H Liu, J Yang, M Wang, L Xue, KC Chou The Protein Journal 24, 385-389, 2005 | 84 | 2005 |
| iScore: a novel graph kernel-based function for scoring protein–protein docking models C Geng, Y Jung, N Renaud, V Honavar, AMJJ Bonvin, LC Xue Bioinformatics 36 (1), 112-121, 2020 | 71 | 2020 |
| Machine learning competition in immunology–Prediction of HLA class I binding peptides GL Zhang, HR Ansari, P Bradley, GC Cawley, T Hertz, X Hu, N Jojic, ... Journal of immunological methods 374 (1-2), 1-4, 2011 | 66 | 2011 |
| Feature selection for multi-class problems using support vector machines GZ Li, J Yang, GP Liu, L Xue PRICAI 2004: Trends in Artificial Intelligence: 8th Pacific Rim …, 2004 | 64 | 2004 |
| 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 | 63 | 2017 |
| Protein–ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3 PI Koukos, LC Xue, AMJJ Bonvin Journal of computer-aided molecular design 33, 83-91, 2019 | 38 | 2019 |
| PANDORA: a fast, anchor-restrained modelling protocol for peptide: MHC complexes DF Marzella, FM Parizi, D Tilborg, N Renaud, D Sybrandi, R Buzatu, ... Frontiers in Immunology 13, 878762, 2022 | 32 | 2022 |
Alexandre M.J.J. BonvinUtrecht universityVerified email at uu.nl