F2Dock：快速傅里叶蛋白-蛋白对接。
F2Dock: fast Fourier protein-protein docking.
机构信息
Computational Visualization Center, Department of Computer Sciences and the Institute of Computational Engineering and Sciences, University of Texas at Austin, 1 University Station C0500, Austin, Texas 78712, USA.
出版信息
IEEE/ACM Trans Comput Biol Bioinform. 2011 Jan-Mar;8(1):45-58. doi: 10.1109/TCBB.2009.57.
The functions of proteins are often realized through their mutual interactions. Determining a relative transformation for a pair of proteins and their conformations which form a stable complex, reproducible in nature, is known as docking. It is an important step in drug design, structure determination, and understanding function and structure relationships. In this paper, we extend our nonuniform fast Fourier transform-based docking algorithm to include an adaptive search phase (both translational and rotational) and thereby speed up its execution. We have also implemented a multithreaded version of the adaptive docking algorithm for even faster execution on multicore machines. We call this protein-protein docking code F2Dock (F2 = Fast Fourier). We have calibrated F2Dock based on an extensive experimental study on a list of benchmark complexes and conclude that F2Dock works very well in practice. Though all docking results reported in this paper use shape complementarity and Coulombic-potential-based scores only, F2Dock is structured to incorporate Lennard-Jones potential and reranking docking solutions based on desolvation energy .
蛋白质的功能通常通过它们的相互作用来实现。确定一对蛋白质及其构象的相对转换，形成稳定的复合物，在自然界中可重复，这被称为对接。它是药物设计、结构确定以及理解功能和结构关系的重要步骤。在本文中，我们将基于非均匀快速傅里叶变换的对接算法扩展到包括自适应搜索阶段（平移和旋转），从而加快其执行速度。我们还实现了自适应对接算法的多线程版本，以便在多核机器上更快地执行。我们将这个蛋白质-蛋白质对接代码称为 F2Dock（F2 = 快速傅里叶变换）。我们已经根据基准复合物列表的广泛实验研究对 F2Dock 进行了校准，并得出结论，F2Dock 在实践中效果非常好。尽管本文报告的所有对接结果仅使用形状互补性和基于库仑势的评分，但 F2Dock 的结构是为了包含 Lennard-Jones 势，并根据去溶剂化能重新对对接解决方案进行排名。
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