SKEMPI2: Experimentally Measured Protein Binding Affinity Changes Upon Mutation

SKEMPI v2 is a manually curated benchmark of experimentally measured changes in protein-protein binding affinity, kinetics, and thermodynamics upon mutation. The dataset focuses on structurally resolved protein-protein interactions, linking mutations to PDB complexes and literature-derived binding measurements. It was authored by LiteFold and last updated on 2026-05-27.

Use Cases

• Evaluating predictive models for mutation effects on protein interfaces based on the described binding affinity changes.
• Training models to predict changes in binding free energy based on the dataset's thermodynamic measurements.
• Benchmarking algorithms for protein complex stability prediction using the curated mutation data.
• Studying relationships between protein structure and binding kinetics using the structurally resolved interaction data.

Strengths

• Manually curated, which suggests a focus on data accuracy and reliability.
• Links mutations to structurally resolved PDB complexes, providing a structural context.
• Includes multiple experimental measurement types: binding affinity, kinetics, and thermodynamics.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment.
• Description metadata is limited; actual data quality requires manual inspection after download.

Provenance

Source

huggingface

Collection Method

Manually curated from literature and structural databases.

Freshness

Last updated 2026-05-27 13:14:26; freshness should be verified.