SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models

Moal, Iain H.; Fernández-Recio, Juan

doi:10.1093/bioinformatics/bts489

Cited by 281Protein Structure and Dynamicsthermodynamics and calorimetric analysesEnzyme Structure and Function

SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models

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Moal, Iain H., Fernández-Recio, Juan·2012·Bioinformatics

DOI 10.1093/bioinformatics/bts489

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Abstract

Motivation: Empirical models for the prediction of how changes in sequence alter protein–protein binding kinetics and thermodynamics can garner insights into many aspects of molecular biology. However, such models require empirical training data and proper validation before they can be widely applied. Previous databases contained few stabilizing mutations and no discussion of their inherent biases or how this impacts model construction or validation. Results: We present SKEMPI, a database of 3047 binding free energy changes upon mutation assembled from the scientific literature, for protein–protein heterodimeric complexes with experimentally determined structures. This represents over four times more data than previously collected. Changes in 713 association and dissociation rates and 127 enthalpies and entropies were also recorded. The existence of biases towards specific mutations, residues, interfaces, proteins and protein families is discussed in the context of how the data can be used to construct predictive models. Finally, a cross-validation scheme is presented which is capable of estimating the efficacy of derived models on future data in which these biases are not present. Availability: The database is available online at http://life.bsc.es/pid/mutation_database/ Contact: juanf@bsc.es

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Other, more specialized, resources exist such as Ab-Bind, which hold data on 1101 mutations across 32 antibody complexes, and SKEMPI, which curates binding energy data for available structures but is not limited to antibody information only.
“Other, more specialized, resources exist such as Ab-Bind [19], which hold data on 1101 mutations across 32 antibody complexes, and SKEMPI [55], which curates binding energy data for available structures but is not limited to antibody information only.”
From Computational approaches to therapeutic antibody design: established methods and emerging trends (2020) · cites this paper as [55]
SKEMPI contains 3,047 mutation data entries for protein-protein heterodimeric complexes with experimentally determined structures.
“SKEMPI is a more general database for protein–protein binding affinity changes following mutation (ΔΔG)11, it contains 3,047 mutation data entries for protein–protein heterodimeric complexes with experimentally determined structures.”
From A topology-based network tree for the prediction of protein–protein binding affinity changes following mutation (2020) · cites this paper as [11]
The SKEMPI dataset contains 2,317 single point mutation data entries (SKEMPI S2317 set).
“There are 2,317 single point mutation data entries among the whole database, which are referred to as the SKEMPI S2317 set.”
From A topology-based network tree for the prediction of protein–protein binding affinity changes following mutation (2020) · cites this paper as [11]

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“Other, more specialized, resources exist such as Ab-Bind [19], which hold data on 1101 mutations across 32 antibody complexes, and SKEMPI [55], which curates binding energy data for available structures but is not limited to antibody information only.”
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Authors: Moal, I. H., & Fernández-Recio, J.
Affiliations: Barcelona Supercomputing Center (ES)
Joint BSC-IRB Research Program in Computational Biology, Life Science Department, Barcelona Supercomputing Center, C/Jordi Girona 29, 08034 Barcelona, Spain
ORCID: Moal, Iain H.
Venue: Bioinformatics
Publisher: Oxford University Press (OUP)
Published: 2012-08-01
Volume: 28
Issue: 20
Pages: 2600-2607
ISSN: 1367-4803 (ISSN-L)
1367-4811
DOI: 10.1093/bioinformatics/bts489
OpenAlex: W2157807259
Cited by: 281
References: 70
Citations by year: 2026: 6 · 2025: 23 · 2024: 26 · 2023: 29 · 2022: 15 · 2021: 19 · 2020: 19 · 2019: 14 · 2018: 38 · 2017: 19 · 2016: 17 · 2015: 24 · 2014: 17 · 2013: 14
FWCI: 7.06
Type: journal article
Language: en
Open access: bronze
doi.org
Locations: Bioinformatics (publishedVersion)
PubMed (publishedVersion)
Funders: Ministerio de Ciencia e Innovación
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Physical Sciences › Chemistry › Physical and Theoretical Chemistry › thermodynamics and calorimetric analyses
Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
Keywords: protein-protein binding, stabilizing mutations, association and dissociation rates, enthalpy and entropy changes, binding kinetics, binding thermodynamics, empirical model, data bias, cross-validation, mutation database
MeSH terms: Kinetics, Models, Chemical, Protein Binding, Thermodynamics, Protein Interaction Mapping, Databases, Protein, Mutant Proteins

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SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models

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