General Information
| Description | A Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models |
| Homepage | http://life.bsc.es/pid/mutation_database/ |
Publications
SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models
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
Related Tools
BDVal
Published August 2010
Reproducible large-scale predictive model development and validation in high-throughput datasets
Rchange
Published February 2012
Algorithms for computing energy changes of RNA secondary structures in response to base mutations
STRUM
Published June 2016
Structure-based prediction of protein stability changes upon single-point mutation
FAIR Evaluation
Sorry, you must be signed in to evaluate this object.
