Barak Raveh在2010年就提出了利用Fragment采样的方法来进行模拟多肽的骨架柔性,在2011年正式发布了FlexPepDock ab-initio的方法流,在40组多肽复合物的测试集合中,25个案例的近天然复合物构象被模拟正确,在当时其性能远超出于其他的计算方法,此后,该方法并未做太多的重大更新,近期(2017年), Nawsad使用其课题组开发的...
FlexPepDock 是一个基于赌徒算法(Monti-Carlo)的多肽分子对接优化的web server (并非基于牛顿力学的分子动力学模拟优化). 它目前主要支持天然氨基酸多肽的对接结果的优化。 http://flexpepdock.furmanlab.cs.huji.ac.il/flexpepdock.furmanlab.cs.huji.ac.il/ FlexPepDock Server 这里我们只讨论天然氨基酸的多...
PaFlexPepDock: Parallel Ab-initio docking of peptides onto their receptors with full flexibility based on Rosetta. Plos One 9, URL http://dx.plos.org/10.1371/journal.pone.0094769 (2014).Li, H.; Lu, L.; Chen, R.; Quan, L.; Xia, X.; Lu, Q....
Rosetta FlexPepDock ab-initio is a structure-based computational protocol able to evaluate peptide-receptor interaction where no prior information of the peptide backbone is known. We benchmarked FlexPepDock ab-initio for docking canonical peptides to MHC-I, and illustrate for the first time the ...
Comparison of PaFlexPepDock and abFlexPepDock on pep_if.Haiou, LiLiyao, LuRong, ChenLijun, QuanXiaoyan, XiaQiang, Lu
Comparison of the performance of HADDOCK and FlexPepDock.Mikael TrelletAdrien S. J. MelquiondAlexandre M. J. J. Bonvin
Correction: PaFlexPepDock: Parallel Ab-Initio Docking of Peptides onto Their Receptors with Full Flexibility Based on Rosetta.doi:10.1371/journal.pone.0105715CorrectionEBSCO_AspPlos One
Marc F. LensinkOra Schueler-FurmanProteins《Proteins-structure Function & Bioinformatics》Marcu, O. et al. (2017) FlexPepDock lessons from CAPRI peptide-protein rounds and suggested new criteria for assessment of model quality and utility. Proteins 85, 445-462...
RosettaPeptide-protein docking is challenging due to the considerable conformational freedom of the peptide. CAPRI rounds 38-45 included two peptide-protein interactions, both characterized by a peptide forming an additional beta strand of a beta sheet in the receptor. Using the Rosetta FlexPepDock ...
Step 3. Submit the modified file to FlexPepDock Now you just go through a quick registration process on thewebserverand add your docking output to the server one by one. You are allowed to submit a maximum of 5 jobs at a time. You may need to wait for some time maybe 10 hours or...