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PepSite:从蛋白质表面预测肽结合位点。

PepSite: prediction of peptide-binding sites from protein surfaces.

机构信息

CellNetworks, University of Heidelberg, 69120 Heidelberg, Germany.

出版信息

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W423-7. doi: 10.1093/nar/gks398. Epub 2012 May 16.

DOI:10.1093/nar/gks398
PMID:22600738
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC3394340/
Abstract

Complex biological functions emerge through intricate protein-protein interaction networks. An important class of protein-protein interaction corresponds to peptide-mediated interactions, in which a short peptide stretch from one partner interacts with a large protein surface from the other partner. Protein-peptide interactions are typically of low affinity and involved in regulatory mechanisms, dynamically reshaping protein interaction networks. Due to the relatively small interaction surface, modulation of protein-peptide interactions is feasible and highly attractive for therapeutic purposes. Unfortunately, the number of available 3D structures of protein-peptide interfaces is very limited. For typical cases where a protein-peptide structure of interest is not available, the PepSite web server can be used to predict peptide-binding spots from protein surfaces alone. The PepSite method relies on preferred peptide-binding environments calculated from a set of known protein-peptide 3D structures, combined with distance constraints derived from known peptides. We present an updated version of the web server that is orders of magnitude faster than the original implementation, returning results in seconds instead of minutes or hours. The PepSite web server is available at http://pepsite2.russelllab.org.

摘要

复杂的生物功能是通过错综复杂的蛋白质-蛋白质相互作用网络出现的。一类重要的蛋白质-蛋白质相互作用对应于肽介导的相互作用,其中一个伴侣的短肽段与另一个伴侣的大蛋白质表面相互作用。蛋白质-肽相互作用通常亲和力较低,参与调节机制,动态重塑蛋白质相互作用网络。由于相对较小的相互作用表面,调节蛋白质-肽相互作用是可行的,并且对于治疗目的非常有吸引力。不幸的是,可用的蛋白质-肽界面的三维结构数量非常有限。对于典型的情况下,感兴趣的蛋白质-肽结构不可用,PepSite 网络服务器可用于仅从蛋白质表面预测肽结合点。PepSite 方法依赖于从一组已知的蛋白质-肽 3D 结构计算出的优选肽结合环境,结合来自已知肽的距离约束。我们呈现了该网络服务器的更新版本,其速度比原始实现快几个数量级,结果在几秒钟内返回,而不是几分钟或几小时。PepSite 网络服务器可在 http://pepsite2.russelllab.org 获得。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5f35/3394340/1c4d85e3fa72/gks398f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5f35/3394340/1c4d85e3fa72/gks398f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5f35/3394340/1c4d85e3fa72/gks398f1.jpg

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