期刊
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
卷 46, 期 2, 页码 190-196出版社
WILEY
DOI: 10.1002/prot.10031
关键词
pair potentials; knowledge-based potentials; protein association; protein-protein interaction; protein recognition
Calculating protein-protein interaction energies is crucial for understanding protein-protein associations. On the basis of the methodology of mean-field potential, we have developed an empirical approach to estimate binding free energy for protein-protein interactions. This knowledge-based approach has been used to derive distance-dependent free energies of protein complexes from a nonredundant training set in the Protein Data Bank (PDB), with a careful treatment of homology. We calculate atom pair potentials for 16 pair interactions, which can reflect the importance of hydrophobic interactions and specific hydrogen-bonding interactions. The derived potentials for hydrogen-bonding interactions show a valley of favorable interactions at a distance of approximate to3 Angstrom, corresponding to that of an established hydrogen bond. For the test set of 28 protein complexes, the calculated energies have a correlation coefficient of 0.75 compared with experimental binding free energies. The performance of the method in ranking the binding energies of different protein-protein complexes shows that the energy estimation can be applied to value binding free energies for protein-protein associations. Proteins 2002;46:190-196. (C) 2001 Wiley-Liss, Inc.
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