PepComposer: computational design of peptides binding to a given protein surface.
PepComposer: computational design of peptides binding to a given protein surface.
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DOI：
10.1093/nar/gkw366
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发表时间：
2016-07-08
影响因子：
14.9
通讯作者：
Tramontano A
中科院分区：
文献类型：
--
作者：
Obarska-Kosinska A;Iacoangeli A;Lepore R;Tramontano A
人们对设计能够与蛋白质的特定区域结合的肽产生了广泛的兴趣，目的是干扰已知的相互作用或作为设计抑制剂的起点。在这里，我们描述PepComposer，一个新的管道结合到一个给定的蛋白质表面的肽的计算设计。PepComposer只需要目标蛋白质结构和结合位点的近似定义作为输入。我们首先检索一组肽骨架骨架支架从单体蛋白质，具有相同的骨架安排作为目标蛋白质的结合位点。接下来，我们为所鉴定的肽支架设计最佳序列。该方法是全自动的，并可作为Web服务器在www.example.com。
There is a wide interest in designing peptides able to bind to a specific region of a protein with the aim of interfering with a known interaction or as starting point for the design of inhibitors. Here we describe PepComposer, a new pipeline for the computational design of peptides binding to a given protein surface. PepComposer only requires the target protein structure and an approximate definition of the binding site as input. We first retrieve a set of peptide backbone scaffolds from monomeric proteins that harbor the same backbone arrangement as the binding site of the protein of interest. Next, we design optimal sequences for the identified peptide scaffolds. The method is fully automatic and available as a web server at http://biocomputing.it/pepcomposer/webserver.