SKEMPI 2.0: an updated benchmark of changes in protein–protein binding energy, kinetics and thermodynamics upon mutation

Abstract

Motivation Understanding the relationship between the sequence, structure, binding energy, binding kinetics and binding thermodynamics of protein–protein interactions is crucial to understanding cellular signaling, the assembly and regulation of molecular complexes, the mechanisms through which mutations lead to disease, and protein engineering. Results We present SKEMPI 2.0, a major update to our database of binding free energy changes upon mutation for structurally resolved protein–protein interactions. This version now contains manually curated binding data for 7085 mutations, an increase of 133%, including changes in kinetics for 1844 mutations, enthalpy and entropy changes for 443 mutations, and 440 mutations, which abolish detectable binding. Availability and implementation The database is available as supplementary data and at https://life.bsc.es/pid/skempi2/. Supplementary information Supplementary data are available at Bioinformatics online.

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• Advances in Molecular Dynamics Simulations and Enhanced Sampling Methods for the Study of Protein Systems · 2020
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• Computational approaches to therapeutic antibody design: established methods and emerging trends · 2019
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• mCSM-PPI2: predicting the effects of mutations on protein–protein interactions · 2019
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