基于快速傅里叶变换的蛋白质-蛋白质对接程序的研究进展

Research Progress in FFT Based Protein-Protein Docking Programs

蛋白质-蛋白质相互作用与识别的研究是分子生物学领域的重要课题。然而由于蛋白质分子巨大,即使将蛋白质看成刚体,在没有指导信息的情况下,系统地搜寻和评估上亿个可能的对接取向十分困难,人们为了解决这个难点,发展了许多搜寻算法,快速傅里叶变换(Fast fourier transform,FFT)便是其中最为流行的算法之一。而打分函数与蛋白质对接结果的准确性密切相关,也是蛋白质-蛋白质对接的难点之一。该文概述了基于快速傅里叶变换的蛋白质-蛋白质对接程序的一般过程。同时,概述了使用与FFT算法的打分函数的一般特征,并且以形状互补、静电力、去溶剂化和统计势能3类介绍了典型的FFT算法下的打分函数。

Protein-protein interactions and their recognition are an important issue in molecular biology. Studying protein-proteininteractions is critical for clarifying biological function, elucidating disease development and related drug design. Nowadays, the experimentally determination of structures of protein complexes is still difficult. Thus, predicting the binding mode between molecular in silico has been greatly concerned. However, the size of most proteins makes it a tough task to computationally feasible to systematically explore and evaluate billions of trial orientations without using any a priori information on the expected structure, even when treating the proteins as rigid bodies. Therefore, many interesting ways of searching the rigid body space have been developed. The Fast Fourier Transform is one of the most popular means. Similarly, scoring, a determination factor of protein docking, is also one of difficulties in docking. In this review, the progress in FFT based protein-protein docking programs,including FrDOCK, DOT, MolFit, GRAMM. ZDOCK, PIPER, F2Dock, ASPDock, HEX, FRODOCK, and SDOCK, is introduced. The general process of FFT based protein-protein docking program is also involved. In the aspect of scoring function, this page outlines the general characteristics of the scoring functions applicable to FFT algorithm, and illustrates typical FFT based scoring functions in three categories （ shape complementarity, electrostatics, desolvation and statistical potentials）.