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Computational prediction of protein interfaces: A review of data driven methods
Author(s) -
Xue Li C.,
Dobbs Drena,
Bonvin Alexandre M.J.J.,
Honavar Vasant
Publication year - 2015
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1016/j.febslet.2015.10.003
Subject(s) - computer science , interface (matter) , protein–protein interaction , docking (animal) , protein structure prediction , computational biology , protein structure , amino acid residue , machine learning , chemistry , biology , peptide sequence , biochemistry , medicine , nursing , bubble , maximum bubble pressure method , parallel computing , gene
Reliably pinpointing which specific amino acid residues form the interface(s) between a protein and its binding partner(s) is critical for understanding the structural and physicochemical determinants of protein recognition and binding affinity, and has wide applications in modeling and validating protein interactions predicted by high‐throughput methods, in engineering proteins, and in prioritizing drug targets. Here, we review the basic concepts, principles and recent advances in computational approaches to the analysis and prediction of protein–protein interfaces. We point out caveats for objectively evaluating interface predictors, and discuss various applications of data‐driven interface predictors for improving energy model‐driven protein–protein docking. Finally, we stress the importance of exploiting binding partner information in reliably predicting interfaces and highlight recent advances in this emerging direction.