Protein docking prediction using predicted protein-protein interface.
Protein docking prediction using predicted protein-protein interface.
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DOI：
10.1186/1471-2105-13-7
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发表时间：
2012-01-10
影响因子：
3
通讯作者：
Kihara D
中科院分区：
文献类型：
--
作者：
Li B;Kihara D
许多重要的细胞过程都是由蛋白质复合物进行的。为了提供相互作用蛋白质的物理图像，过去已经开发了许多计算蛋白质-蛋白质预测方法。然而，在替代构象中识别顶级的正确对接复杂结构仍然很困难。我们提出了一种新颖的蛋白质对接算法，该算法利用不完美的蛋白质-蛋白质结合界面预测来指导蛋白质对接。由于蛋白质结合位点预测的准确性因情况而异，因此面临的挑战是开发一种方法，通过使用可能不是 100% 准确的结合位点预测，不会恶化而是改善对接结果。该算法名为 PI-LZerD（使用带有本地 3D Zernike 描述符的对接算法的预测接口），基于我们之前开发的成对蛋白质对接预测算法 LZerD。 PI-LZerD首先使用提供的蛋白质-蛋白质结合界面预测作为约束进行对接预测，然后使用更新的对接界面信息进行第二轮对接，以进一步改善对接构象。结合和未结合情况的基准结果表明，与不使用结合位点预测或使用结合位点预测作为后过滤的对接相比，PI-LZerD 一致提高了对接预测的准确性。我们开发了PI-LZerD，一种成对对接算法，它利用不完美的蛋白质-蛋白质结合界面预测来提高对接精度。在一系列基准实验中，包括使用实际对接接口位点预测以及未绑定对接情况进行对接，PI-LZerD 始终表现出比其他方法更好的预测精度。
Many important cellular processes are carried out by protein complexes. To provide physical pictures of interacting proteins, many computational protein-protein prediction methods have been developed in the past. However, it is still difficult to identify the correct docking complex structure within top ranks among alternative conformations. We present a novel protein docking algorithm that utilizes imperfect protein-protein binding interface prediction for guiding protein docking. Since the accuracy of protein binding site prediction varies depending on cases, the challenge is to develop a method which does not deteriorate but improves docking results by using a binding site prediction which may not be 100% accurate. The algorithm, named PI-LZerD (using Predicted Interface with Local 3D Zernike descriptor-based Docking algorithm), is based on a pair wise protein docking prediction algorithm, LZerD, which we have developed earlier. PI-LZerD starts from performing docking prediction using the provided protein-protein binding interface prediction as constraints, which is followed by the second round of docking with updated docking interface information to further improve docking conformation. Benchmark results on bound and unbound cases show that PI-LZerD consistently improves the docking prediction accuracy as compared with docking without using binding site prediction or using the binding site prediction as post-filtering. We have developed PI-LZerD, a pairwise docking algorithm, which uses imperfect protein-protein binding interface prediction to improve docking accuracy. PI-LZerD consistently showed better prediction accuracy over alternative methods in the series of benchmark experiments including docking using actual docking interface site predictions as well as unbound docking cases.
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通讯作者：
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