Performance and Its Limits in Rigid Body Protein-Protein Docking
Performance and Its Limits in Rigid Body Protein-Protein Docking
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DOI：
10.1016/j.str.2020.06.006
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发表时间：
2020-09-01
期刊：
影响因子：
5.7
通讯作者：
Vajda, Sandor
中科院分区：
文献类型：
--
作者：
Desta, Israel T.;Porter, Kathryn A.;Vajda, Sandor
快速傅立叶变换（FFT）算法的开发使数十亿个复杂构型的取样，从而彻底改变了蛋白质 - 蛋白质对接。现在，基于FFT的方法已广泛可用，并且已在数十万个对接计算中使用。尽管该方法执行“软”对接，从而使组件蛋白有些重叠，但刚体的假设清楚地引入了对准确性和可靠性的限制。此外，该方法只能与相关函数总和表示的能量表达式使用。在本文中，我们使用良好的蛋白质 - 蛋白质对接基准测试基准设置来评估这些限制的结果，这是通过关注对接服务器cluspro的性能，该服务器cluspro的性能实现了最好的刚体方法之一。此外，我们在使用既定能量术语进行评分时，与灵活的对接算法进行比较并回顾CAPRI对接实验中服务器的历史性能时探讨了准确性的理论限制。
The development of fast Fourier transform (FFT) algorithms enabled the sampling of billions of complex conformations and thus revolutionized protein-protein docking. FFT-based methods are now widely available and have been used in hundreds of thousands of docking calculations. Although the methods perform "soft" docking, which allows for some overlap of component proteins, the rigid body assumption clearly introduces limitations on accuracy and reliability. In addition, the method can work only with energy expressions represented by sums of correlation functions. In this paper we use a well-established protein-protein docking benchmark set to evaluate the results of these limitations by focusing on the performance of the docking server ClusPro, which implements one of the best rigid body methods. Furthermore, we explore the theoretical limits of accuracy when using established energy terms for scoring, provide comparison with flexible docking algorithms, and review the historical performance of servers in the CAPRI docking experiment.