Development of unified statistical potentials describing protein-protein interactions
Development of unified statistical potentials describing protein-protein interactions
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DOI：
10.1016/s0006-3495(03)74997-2
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发表时间：
2003-03-01
影响因子：
3.4
通讯作者：
Skolnick, J
中科院分区：
文献类型：
--
作者：
Lu, H;Lu, L;Skolnick, J
发展了一个基于残基和基于重原子的统计对势，用于评估蛋白质-蛋白质相互作用的强度。为了保证潜力的质量，构建了一个无冗余的高质量二聚体数据库。通过文献搜索来检查这个数据集中的蛋白质复合体，以确认它们形成了多聚体，并分析了跨越蛋白质-蛋白质界面相互作用的成对氨基酸偏好，并构建了对电势。基于残基的势的性能是通过使用四个折刀测试和评估势从错误的蛋白质-蛋白质界面中选择真的蛋白质-蛋白质界面的能力来评估的。与用于单体蛋白质结构预测的势相比，结构域间势在区分蛋白质-蛋白质相互作用方面表现得更好。从同二聚体界面得到的电势与从杂二聚体界面得到的电势基本相同，相关系数为0.92。基于残基的潜力非常适合于基因组规模的蛋白质相互作用的预测和分析，例如最近开发的基于线程的算法MULTIPROSPECTOR。然而，基于原子的势越耗时，在从对接产生的诱饵中识别接近自然的结构时表现得越好。
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.