Interactions · Database
SKEMPI 2
A database of protein–protein binding free energy and kinetic changes upon mutation for solved complexes.
What SKEMPI 2 is
SKEMPI 2 (Structural database of Kinetics and Energetics of Mutant Protein Interactions version 2.0) is a curated database of changes in thermodynamic parameters and kinetic rate constants caused by mutations. It focuses on protein–protein interactions where an experimental structure of the complex has been resolved and deposited in the Protein Data Bank (PDB).
Developed by J. Jankauskaitė, B. Jiménez-García, J. Dapkūnas, J. Fernández-Recio, and I. H. Moal, the resource provides an updated benchmark dataset. It serves computational biologists and biophysicists by providing training and validation data for algorithms designed to predict mutation-induced changes in binding affinity.
How it is organised
SKEMPI 2 organises experimentally measured binding free energy changes, thermodynamic parameters, and kinetic rate constants alongside corresponding complex structures from the Protein Data Bank. Cleaned PDB structures are provided for the represented complexes.
The platform allows researchers to browse entries online, review summary statistics, download the complete dataset, and submit new mutation data.
Key facts
- Total mutations
- 7,085
- Data category
- Interaction
- Measurement types
- Thermodynamic parameters and kinetic rate constants
- Structural requirement
- Solved complex structure in the Protein Data Bank (PDB)
What you can use it for
- Training affinity predictors
- Use the curated mutation sets to train and validate machine learning models or scoring functions that estimate binding affinity changes upon mutation.
- Analysing interaction kinetics and thermodynamics
- Investigate how amino acid substitutions alter rate constants and binding free energy in structurally defined protein–protein complexes.
Strengths and limits
Good at
- Connects kinetic and thermodynamic mutation measurements directly to three-dimensional structures from the Protein Data Bank.
- Provides a standardized benchmark covering 7,085 mutations across resolved protein–protein complexes.
Watch out for
- Restricted only to protein–protein interactions that have an experimentally solved complex structure available in the Protein Data Bank.
Questions
Can I search SKEMPI 2 without writing code?
SKEMPI 2 is catalogued here but not yet queried live, so the agent can point you to it but cannot search it for you yet.
Can I reuse data from SKEMPI 2?
SKEMPI 2 publishes its own terms of use; read them on https://life.bsc.es/pid/skempi2 before reusing its records.
What information does SKEMPI 2 record?
It records changes in thermodynamic parameters and kinetic rate constants resulting from mutations in protein–protein complexes.
Are structural models available for all records?
Every entry corresponds to an interaction with an experimentally determined complex structure available in the Protein Data Bank, and the repository includes cleaned PDB structures.
How many mutations are catalogued in the database?
SKEMPI version 2.0 contains 7,085 recorded mutations.
How to cite it
Jankauskaitė J, Jiménez-García B, Dapkūnas J, Fernández-Recio J, Moal IH (2019) SKEMPI 2.0: an updated benchmark of changes in protein–protein binding energy, kinetics and thermodynamics upon mutation. Bioinformatics 35, 462–469 ( https://doi.org/10.1093/bioinformatics/bty635 )
Written from SKEMPI 2's own website and reference material. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.