ZDOCK: An initial-stage protein-docking algorithm
ZDOCK: An initial-stage protein-docking algorithm
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DOI：
10.1002/prot.10389
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发表时间：
2003-07-01
影响因子：
2.9
通讯作者：
Weng, ZP
中科院分区：
文献类型：
--
作者：
Chen, R;Li, L;Weng, ZP
评分函数的建立对蛋白质对接具有重要意义。在这里，我们提出了一个新的评分功能的初始阶段的未绑定对接。它结合了我们最近开发的成对形状互补性与去溶剂化和静电。我们比较了这个评分功能与其他三个功能的一个大的基准49个非冗余的测试用例，并显示其上级性能，特别是抗体-抗原类别的测试用例。对于44个测试用例（基准测试的90%），在6度旋转采样密度下，我们可以在前2000个预测中保留至少一个近原生结构，平均每个测试用例有52个近原生结构。剩下的五个困难的测试案例可以解释为结合亲和力差，大的骨架构象变化，以及我们的算法的强烈倾向于识别大凹结合口袋的组合。所有四个评分函数都已集成到我们基于快速傅立叶变换的对接算法ZDOCK中，学术用户可以在http://zlab.bu.edu/similar torongtdock上免费获得该算法。(C)2003 Wiley-Liss，Inc.
The development of scoring functions is of great importance to protein docking. Here we present a new scoring function for the initial stage of unbound docking. It combines our recently developed pairwise shape complementarity with desolvation and electrostatics. We compare this scoring function with three other functions on a large benchmark of 49 nonredundant test cases and show its superior performance, especially for the antibody-antigen category of test cases. For 44 test cases (90% of the benchmark), we can retain at least one near-native structure within the top 2000 predictions at the 6degrees rotational sampling density, with an average of 52 near-native structures per test case. The remaining five difficult test cases can be explained by a combination of poor binding affinity, large backbone conformational changes, and our algorithm's strong tendency for identifying large concave binding pockets. All four scoring functions have been integrated into our Fast Fourier Transform based docking algorithm ZDOCK, which is freely available to academic users at http://zlab.bu.edu/similar torongtdock. (C) 2003 Wiley-Liss, Inc.