Docking macromolecules with flexible segments
Docking macromolecules with flexible segments
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DOI：
10.1002/jcc.10329
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发表时间：
2003-11-30
影响因子：
3
通讯作者：
Prévost, C
中科院分区：
文献类型：
--
作者：
Bastard, K;Thureau, A;Prévost, C
我们解决了一个主要障碍，大分子对接算法，提出了一种新的方法，考虑到诱导的构象调整位于蛋白质/大分子界面的柔性环。该方法，MC 2，是基于一个多拷贝表示的循环，再加上Monte Carlo构象搜索的相对位置的大分子和它们的侧链构象。最佳环构象的选择在Monte Carlo循环期间通过迭代调整每个拷贝的权重来进行。本文描述了该方法的参数化和对已知3-D结构的蛋白质-DNA复合物的试验，涉及果蝇prd配对结构域蛋白及其靶寡核苷酸[Wenqing，X.例如，Cell 1995，80，639]。我们证明了我们的算法可以正确地配置和定位这种蛋白质，尽管它与DNA的两个凹槽的相互作用相对复杂。(C)2003 Wiley Periodicals，Inc.
We address a major obstacle to macromolecular docking algorithms by presenting a new method that takes into account the induced conformational adjustment of flexible loops situated at a protein/macromolecule interface. The method, MC2, is based on a multiple copy representation of the loops, coupled with a Monte Carlo conformational search of the relative position of the macromolecules and their side chain conformations. The selection of optimal loop conformations takes place during Monte Carlo cycling by the iterative adjustment of the weight of each copy. We describe here the parameterization of the method and trials on a protein-DNA complex of known 3-D structure, involving the Drosophila prd paired domain protein and its target oligonucleotide [Wenqing, X. et al., Cell 1995, 80, 639]. We demonstrate that our algorithm can correctly configure and position this protein, despite its relatively complex interactions with both grooves of DNA. (C) 2003 Wiley Periodicals, Inc.