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Bio-Protocol|August 30, 2021
PRODIGY: A Contact-based Predictor of Binding Affinity in Protein-protein ComplexesAnna Vangone, Alexandre M J J BonvinProtein Engineering, Design & Selection : PEDS|June 11, 2016
Exploring the interplay between experimental methods and the performance of predictors of binding affinity change upon mutations in protein complexesCunliang Geng, Anna Vangone, Alexandre M J J BonvinBMC Bioinformatics|December 1, 2018
Distinguishing crystallographic from biological interfaces in protein complexes: role of intermolecular contacts and energetics for classificationKatarina Elez, Alexandre M J J Bonvin, Anna VangoneProteins|November 13, 2018
iSEE: Interface structure, evolution, and energy-based machine learning predictor of binding affinity changes upon mutationsCunliang Geng, Anna Vangone, Gert E Folkers, et al.Bioinformatics (Oxford, England)|May 4, 2019
Large-scale prediction of binding affinity in protein-small ligand complexes: the PRODIGY-LIG web serverAnna Vangone, Joerg Schaarschmidt, Panagiotis Koukos, et al.Current Opinion in Structural Biology|February 21, 2006
Flexible protein-protein dockingAlexandre M J J BonvinJournal of Biomolecular NMR|June 1, 2011
Protein-protein HADDocking using exclusively pseudocontact shiftsChristophe Schmitz, Alexandre M J J BonvinStructure (London, England : 1993)|April 13, 2011
A multidomain flexible docking approach to deal with large conformational changes in the modeling of biomolecular complexesEzgi Karaca, Alexandre M J J BonvinMethods in Molecular Biology (Clifton, N.J.)|July 2, 2025
Ranking Protein-Protein Models with Large Language Models and Graph Neural NetworksXiaotong Xu, Alexandre M J J BonvinBriefings in Bioinformatics|July 12, 2026
AbTune: layer-wise selective fine-tuning of protein language models for antibodiesXiaotong Xu, Alexandre M J J BonvinPageof 26