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Bioinformatics. 2019 Feb 1;35(3):462-469. doi: 10.1093/bioinformatics/bty635.

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

Author information

1
Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
2
Barcelona Supercomputing Center (BSC), Barcelona, Spain.
3
Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, the Netherlands.
4
Institut de Biologia Molecular de Barcelona (IBMB), CSIC, Barcelona, Spain.
5
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK.

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.

PMID:
30020414
PMCID:
PMC6361233
DOI:
10.1093/bioinformatics/bty635
[Indexed for MEDLINE]
Free PMC Article

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