FiberDock: a web server for flexible induced-fit backbone refinement in molecular docking.
FiberDock: a web server for flexible induced-fit backbone refinement in molecular docking.
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DOI：
10.1093/nar/gkq373
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发表时间：
2010-07
影响因子：
14.9
通讯作者：
Wolfson HJ
中科院分区：
文献类型：
--
作者：
Mashiach E;Nussinov R;Wolfson HJ
蛋白质-蛋白质对接算法的目标是根据组装蛋白质的原子结构预测复合物的结构，对接过程通常包括两个主要步骤：对接候选物的生成和优化。细化阶段的目的是提高候选解决方案的准确性，并确定其中的近原生解决方案。在蛋白质-蛋白质相互作用期间，侧链和主链都改变其构象。精细化方法应该模拟这些构象变化，以获得更准确的复合物模型。处理蛋白质骨架的灵活性是对接方法的一个主要挑战，因为骨架的灵活性增加了大量的自由度的搜索空间。FiberDock是第一个对接细化Web服务器，它同时考虑了主干和侧链的灵活性。给定一组多达100个潜在的对接候选者，FiberDock对相互作用过程中发生的主链和侧链运动进行建模，细化结构并根据能量函数对其进行评分。FiberDock Web服务器是免费的，无需登录http://bioinfo3d.cs.tau.ac.il/FiberDock/即可使用。
Protein–protein docking algorithms aim to predict the structure of a complex given the atomic structures of the proteins that assemble it. The docking procedure usually consists of two main steps: docking candidate generation and their refinement. The refinement stage aims to improve the accuracy of the candidate solutions and to identify near-native solutions among them. During protein–protein interaction, both side chains and backbone change their conformation. Refinement methods should model these conformational changes in order to obtain a more accurate model of the complex. Handling protein backbone flexibility is a major challenge for docking methodologies, since backbone flexibility adds a huge number of degrees of freedom to the search space. FiberDock is the first docking refinement web server, which accounts for both backbone and side-chain flexibility. Given a set of up to 100 potential docking candidates, FiberDock models the backbone and side-chain movements that occur during the interaction, refines the structures and scores them according to an energy function. The FiberDock web server is free and available with no login requirement at http://bioinfo3d.cs.tau.ac.il/FiberDock/.
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影响因子：
14.9
作者：
Schneidman-Duhovny D;Inbar Y;Nussinov R;Wolfson HJ
通讯作者：
Wolfson HJ
影响因子：
14.9
作者：
Comeau, SR;Gatchell, DW;Camacho, CJ
通讯作者：
Camacho, CJ
影响因子：
2.9
作者：
Chaudhury, Sidhartha;Sircar, Aroop;Gray, Jeffrey J.
通讯作者：
Gray, Jeffrey J.
影响因子：
2.9
作者：
Andrusier, Nelly;Mashiach, Efrat;Nussinov, Ruth;Wolfson, Haim J.
通讯作者：
Wolfson, Haim J.
影响因子：
14.9
作者：
Lindahl E;Azuara C;Koehl P;Delarue M
通讯作者：
Delarue M