de Vries Sjoerd J, Bonvin Alexandre M J J
Faculty of Sciences, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands.
Bioinformatics. 2006 Sep 1;22(17):2094-8. doi: 10.1093/bioinformatics/btl275. Epub 2006 Jun 9.
Some amino acids clearly show preferences over others in protein-protein interfaces. These preferences, or so-called interface propensities can be used for a priori interface prediction. We investigated whether the prediction accuracy could be improved by considering not single but pairs of residues in an interface. Here we present the first systematic analysis of intramolecular surface contacts in interface prediction.
We show that preferences do exist for contacts within and around an interface region within one molecule: specific pairs of amino acids are more often occurring than others. Using intramolecular contact propensities in a blind test, higher average scores were assigned to interface residues than to non-interface residues. This effect persisted as small but significant when the contact propensities were corrected to eliminate the influence of single amino acid interface propensity. This indicates that intramolecular contact propensities may replace interface propensities in protein-protein interface prediction.
The source code is available on request from the authors.
在蛋白质-蛋白质界面中，一些氨基酸相对于其他氨基酸表现出明显的偏好。这些偏好，即所谓的界面倾向，可用于先验界面预测。我们研究了通过考虑界面中的残基对而非单个残基，预测准确性是否能够提高。在此，我们展示了对界面预测中分子内表面接触的首次系统分析。
我们表明，在一个分子的界面区域内及其周围的接触确实存在偏好：特定的氨基酸对比其他氨基酸对更常出现。在一项盲测中使用分子内接触倾向，与非界面残基相比，界面残基被赋予了更高的平均分数。当校正接触倾向以消除单个氨基酸界面倾向的影响时，这种效应仍然存在，虽小但显著。这表明分子内接触倾向可能在蛋白质-蛋白质界面预测中取代界面倾向。
可根据作者要求获取源代码。
