Evaluation of AlphaFold 3's Protein-Protein Complexes for Predicting Binding Free Energy Changes upon Mutation.

ABSTRACT: AlphaFold 3 (AF3), the latest version of protein structure prediction software, goes beyond its predecessors by predicting protein-protein complexes. It could revolutionize drug discovery and protein engineering, marking a major step toward comprehensive, automated protein structure prediction. However, independent validation of AF3's predictions is necessary. In this work, we evaluate AF3 complex structures using the SKEMPI 2.0 database which involves 317 protein-protein complexes and 8338 mutations. AF3 complex structures when applied to the most advanced TDL model, MT-TopLap (MultiTask-Topological Laplacian), give rise to a very good Pearson correlation coefficient of 0.86 for predicting protein-protein binding free energy changes upon mutation, which is slightly less than the 0.88 achi

SUBMITTER: Wee J 

PROVIDER: S-EPMC11351016 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature