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蛋白质三级结构预测算法综述
A Survey on Algorithms for Protein Tertiary Structure Prediction

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王超 1,2   朱建伟 1,2   张海仓 1,2   巩海娥 1,2   郑伟谋 3   卜东波 1  
文摘 了解蛋白质的三维结构对于认识蛋白质的功能有着重要意义.由于蛋白质结构测定的速度远远跟不上蛋白质序列测定的速度,因此使用计算技术依据蛋白质序列预测结构成为结构测定的有力补充.该文首先总结了蛋白质结构预测的3类基本方法,包括基于序列-序列联配的同源建模法、基于序列-结构联配的归范法以及基于最小化能量函数的从头预测法,并分析了其中的关键技术;进而总结了有代表性的蛋白质结构预测软件工具,然后通过对蛋白质结构预测CASP比赛结果的分析比较了各种方法的性能,并获得了如下结论:当待预测蛋白质与模板蛋白质序列等同度超过30%时,同源建模法能够产生高质量的预测结果,归范法中的远同源检测以及从头预测法中的能量函数设计是尚待突破的关键点;最后,该文总结分析了未来的发展趋势,并阐释了强序列信号“绑架”蛋白质构象生成的观点,即从整体来说,蛋白质序列与结构的关联关系并不显著,但其中某些特定的局部序列片段具有非常强的结构倾向性,这些强信号区域引导蛋白质的折叠过程,对这些强信号区域的认识将会有助于提升蛋白质结构预测算法的性能.
其他语种文摘 Proteins are important macromolecules that consist of one or more long chains of amino acids,and perform a great variety of biological functionalities,including catalyzing, transportation,and responses to stimuli.In natural environment,aprotein usually folds into a specific tertiary structural conformation called native structure.The functionalities of a protein are largely determined by its structural conformation,rending the understanding of protein structures fatally important.However,the experimental approaches for the determination of protein structures are commonly labor-intensive and time-consuming,and thus cannot match up the speed of protein sequencing.Therefore,it is invaluable to predict protein structures using computational approaches.In this study,we summarized the popular strategies for protein structure prediction,including homology modeling approaches based on sequence-sequence alignment,threading approaches based on sequence-structure alignment,and ab initio approaches based on optimizing energy functions.Furthermore,we listed the popular software packages for protein structure prediction as well as their performance in the CASP(Critical Assessment of protein Structure Prediction)competition.The evaluation of these approaches showed the following three observations:(1)If the sequence identity between a query protein and a certain template protein exceeds 30%,homology modeling approaches usually report accurate prediction results; (2)For threading approaches,how to improve fold recognition for remote homology proteins remains one of the challenges;and(3)For ab initio approaches,the design of an accurate energy function,together with building structural conformation with the assistance of the information of residue-residue contact information still need investigation.Finally,we summarized this study by listing our perspectives on protein structure prediction,especially on the the perspective that protein folding is an elite-driven process.Specifically,the correlation between protein sequence and its native structure is not that strong from the global point of view;however,at certain regions,local sequences carry strong signals of local structural preference.These regions might initialize the protein folding process,and speed up protein folding through significantly reducing search space of possible structural conformations.The understanding of these regions should greatly facilitate the developing of novel approaches for protein structure prediction.In summary, the accurate prediction of protein structures heavily relies on our insights into the relationship between protein sequence and structure,as well as modeling these insights into an efficient statistical models and algorithms.Protein structure is a representative problem that a linear sequence of entities forms specific complex structures under the interactions among these entities; thus,the advances in the field of protein structure prediction will contribute to solving other similar problems.
来源 计算机学报 ,2018,41(4):760-779 【核心库】
DOI 10.11897/sp.j.1016.2018.00760
关键词 蛋白质结构 ; 同源建模 ; 归范法 ; 从头预测法 ; 能量函数 ; 动态规划 ; 线性规划
地址

1. 中国科学院计算技术研究所, 北京, 100190  

2. 中国科学院大学, 北京, 100049  

3. 中国科学院理论物理研究所, 北京, 100190

语种 中文
文献类型 综述型
ISSN 0254-4164
学科 自动化技术、计算机技术
基金 国家973计划 ;  国家自然科学基金 ;  中国科学院理论物理研究所理论物理国家重点实验室开放工程项目
文献收藏号 CSCD:6214537

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