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...
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 ...
Rosetta FlexPepDock ab-initio: simultaneous folding, docking and refinement of peptides onto their receptors. PLoS One 6, e18934 (2011). CAS PubMed PubMed Central Google Scholar Sedan, Y., Marcu, O., Lyskov, S. & Schueler-Furman, O. Peptiderive server: derive peptide inhibitors from ...
分享收藏 Rosetta FlexPepDock: 柔性多肽对接 谷雨 力文所生物科技有限公司CIO/RosettaAI社区发起人 谷雨: 作者: 吴炜坤 参考1: Rosetta FlexPepDock ab-initio: Simultaneous Folding, Docking and Refinement of Pepti…阅读全文 赞同32 8 条评论 分享收藏 12下一页 ...
Lapidoth, G., Parker, J., Prilusky, J. & Fleishman, S. J. AbPredict 2: a server for accurate and unstrained structure prediction of antibody variable domains.Bioinformatics35, 1591–1593 (2019). CASPubMedGoogle Scholar Sircar, A. & Gray, J. J. SnugDock: paratope structural optimization...
Rosetta FlexPepDock web server—high resolution modeling of peptide–protein interactions Peptide–protein interactions are among the most prevalent and important interactions in the cell, but a large fraction of those interactions lack detailed... L Nir,R Barak,C Eyal,... - 《Nucleic Acids Resear...
FlexPepDock Concurrently samples backbone degrees of freedom on the peptide SymDockProtocol Symmetric oligomer docking RigidBodyTransMover manually manipulate the relative position of two bodies across a jump RigidBodyPerturbNoCenter UnbiasedRigidBodyPerturbNoCenter ...
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
PIPER-FlexPepDock121 是 Rosetta 的全局多肽对接协议。它使用基于 PIPER FFT 的对接122 对片段进行刚体对接,并使用 FlexPepDock123 对复合物进行细化。PIPER-FlexPepDock可以根据多肽序列和自由受体结构生成多肽-蛋白质复合物(图 3f)。在受体具有灵活性的情况下,性能会下降。