ArticleProtein science : a publication of the Protein Society2014
A minimal model of protein-protein binding affinities.
Article in Protein science : a publication of the Protein Society, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- Software for Predicting Binding Free Energy of Protein-Protein Complexes and Their Mutants.Methods in molecular biology (Clifton, N.J.) · 2024Article
- EnCPdock: a web-interface for direct conjoint comparative analyses of complementarity and binding energetics in inter-protein associations.Journal of molecular modeling · 2023Article
- Article
- An expanded benchmark for antibody-antigen docking and affinity prediction reveals insights into antibody recognition determinants.Structure (London, England : 1993) · 2021Article
- A structure-based model for the prediction of protein-RNA binding affinity.RNA (New York, N.Y.) · 2019Article
- An account of solvent accessibility in protein-RNA recognition.Scientific reports · 2018Article
- The Molecular Tweezer CLR01 Stabilizes a Disordered Protein-Protein Interface.Journal of the American Chemical Society · 2017Article
- Novel Structural Parameters of Ig-Ag Complexes Yield a Quantitative Description of Interaction Specificity and Binding Affinity.Frontiers in immunology · 2017Article
- AB-Bind: Antibody binding mutational database for computational affinity predictions.Protein science : a publication of the Protein Society · 2016Article
- Probing binding hot spots at protein-RNA recognition sites.Nucleic acids research · 2016Article
- Destabilization of the dimer interface is a common consequence of diverse ALS-associated mutations in metal free SOD1.Protein science : a publication of the Protein Society · 2015Article
- Article
- Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2.Journal of molecular biology · 2015Article
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Abstract
A minimal model of protein-protein binding affinity that takes into account only two structural features of the complex, the size of its interface, and the amplitude of the conformation change between the free and bound subunits, is tested on the 144 complexes of a structure-affinity benchmark. It yields Kd values that are within two orders of magnitude of the experiment for 67% of the complexes, within three orders for 88%, and fails on 12%, which display either large conformation changes, or a very high or a low affinity. The minimal model lacks the specificity and accuracy needed to make useful affinity predictions, but it should help in assessing the added value of parameters used by more elaborate models, and set a baseline for evaluating their performances.
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