Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Hadassah Medical School, The Hebrew University, Jerusalem 91120, Israel.
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W249-53. doi: 10.1093/nar/gkr431. Epub 2011 May 27.
Peptide-protein interactions are among the most prevalent and important interactions in the cell, but a large fraction of those interactions lack detailed structural characterization. The Rosetta FlexPepDock web server (http://flexpepdock.furmanlab.cs.huji.ac.il/) provides an interface to a high-resolution peptide docking (refinement) protocol for the modeling of peptide-protein complexes, implemented within the Rosetta framework. Given a protein receptor structure and an approximate, possibly inaccurate model of the peptide within the receptor binding site, the FlexPepDock server refines the peptide to high resolution, allowing full flexibility to the peptide backbone and to all side chains. This protocol was extensively tested and benchmarked on a wide array of non-redundant peptide-protein complexes, and was proven effective when applied to peptide starting conformations within 5.5 Å backbone root mean square deviation from the native conformation. FlexPepDock has been applied to several systems that are mediated and regulated by peptide-protein interactions. This easy to use and general web server interface allows non-expert users to accurately model their specific peptide-protein interaction of interest.
肽-蛋白相互作用是细胞中最普遍和最重要的相互作用之一，但其中很大一部分相互作用缺乏详细的结构特征。Rosetta FlexPepDock 网络服务器（http://flexpepdock.furmanlab.cs.huji.ac.il/）为肽-蛋白复合物建模提供了一个高分辨率肽对接（细化）协议的接口，该协议在 Rosetta 框架内实现。给定一个蛋白质受体结构和受体结合位点中肽的近似（可能不准确）模型，FlexPepDock 服务器将肽细化到高分辨率，允许肽骨架和所有侧链完全灵活。该协议在广泛的非冗余肽-蛋白复合物上进行了大量测试和基准测试，并在应用于与天然构象的骨架均方根偏差在 5.5 Å 以内的肽起始构象时被证明是有效的。FlexPepDock 已应用于多个由肽-蛋白相互作用介导和调节的系统。这个易于使用和通用的网络服务器接口允许非专家用户准确地模拟他们感兴趣的特定肽-蛋白相互作用。
