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

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Abstract
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. 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. The database is available as supplementary data and at https://life.bsc.es/pid/skempi2/. Supplementary data are available at Bioinformatics online.
Funding Information
  • European Molecular Biology Laboratory
  • Biotechnology and Biological Sciences Research Council
  • Future Leader Fellowship (BB/N011600/1)
  • Spanish Ministry of Economy and Competitiveness
  • MINECO (BIO2016-79930-R)
  • Interreg POCTEFA (EFA086/15)
  • European Commission (676566)