期刊
BIOPHYSICAL JOURNAL
卷 84, 期 3, 页码 1895-1901出版社
BIOPHYSICAL SOCIETY
DOI: 10.1016/S0006-3495(03)74997-2
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资金
- NCRR NIH HHS [P41 RR012255] Funding Source: Medline
- NIGMS NIH HHS [GM-48835, R01 GM048835, GM RR-12255] Funding Source: Medline
A residue-based and a heavy atom-based statistical pair potential are developed for use in assessing the strength of protein-protein interactions. To ensure the quality of the potentials, a nonredundant, high-quality dimer database is constructed. The protein complexes in this dataset are checked by a literature search to confirm that they form multimers, and the pairwise amino acid preference to interact across a protein-protein interface is analyzed and pair potentials constructed. The performance of the residue-based potentials is evaluated by using four jackknife tests and by assessing the potentials' ability to select true protein-protein interfaces from false ones. Compared to potentials developed for monomeric protein structure prediction, the interdomain potential performs much better at distinguishing protein-protein interactions. The potential developed from homodimer interfaces is almost the same as that developed from heterodimer interfaces with a correlation coefficient of 0.92. The residue-based potential is well suited for genomic scale protein interaction prediction and analysis, such as in a recently developed threading-based algorithm, MULTIPROSPECTOR. However, the more time-consuming atom-based potential performs better in identifying near-native structures from docking generated decoys.
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