INSERM U973, MTi, F-75205 Paris, France Université Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France.
INSERM U973, MTi, F-75205 Paris, France Université Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France Ressource Parisienne en Bioinformatique Structurale, F-75205 Paris, France.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W221-6. doi: 10.1093/nar/gku404. Epub 2014 May 6.
Peptide-protein interactions are important to many processes of life, particularly for signal transmission or regulatory mechanisms. When no information is known about the interaction between a protein and a peptide, it is of interest to propose candidate sites of interaction at the protein surface, to assist the design of biological experiments to probe the interaction, or to serve as a starting point for more focused in silico approaches. PEP-SiteFinder is a tool that will, given the structure of a protein and the sequence of a peptide, identify protein residues predicted to be at peptide-protein interface. PEP-SiteFinder relies on the 3D de novo generation of peptide conformations given its sequence. These conformations then undergo a fast blind rigid docking on the complete protein surface, and we have found, as the result of a benchmark over 41 complexes, that the best poses overlap to some extent the experimental patch of interaction for close to 90% complexes. In addition, PEP-SiteFinder also returns a propensity index we have found informative about the confidence of the prediction. The PEP-SiteFinder web server is available at http://bioserv.rpbs.univ-paris-diderot.fr/PEP-SiteFinder.
肽-蛋白相互作用对生命的许多过程都很重要，特别是对于信号转导或调节机制。当对蛋白质和肽之间的相互作用一无所知时，预测蛋白质表面相互作用的候选位点以协助设计探测相互作用的生物学实验，或者作为更集中的计算方法的起点是很有意义的。PEP-SiteFinder 是一种工具，它可以根据蛋白质的结构和肽的序列，识别预测处于肽-蛋白界面的蛋白质残基。PEP-SiteFinder 依赖于其序列的 3D 从头生成肽构象。然后，这些构象在完整的蛋白质表面上进行快速盲目刚性对接，我们已经发现，通过对 41 个复合物的基准测试，最佳构象在接近 90%的复合物中在某种程度上与实验相互作用的斑块重叠。此外，PEP-SiteFinder 还返回一个倾向性指数，我们发现它对预测的置信度很有帮助。PEP-SiteFinder 网络服务器可在 http://bioserv.rpbs.univ-paris-diderot.fr/PEP-SiteFinder 上获得。
