Identifying Coevolution Between Amino Acid Residues in Protein Families: Advances in the Improvement and Evaluation of Correlated Mutation Algorithms

CORC > 天津工业生物技术研究所 > 结构生物信息学和整合系统生物学实验室宋江宁 > 期刊论文

	Identifying Coevolution Between Amino Acid Residues in Protein Families: Advances in the Improvement and Evaluation of Correlated Mutation Algorithms
	Xu, Haisong 1,2; Li, Xiaoqin 2; Zhang, Ziding 3; Song, Jiangning 1,4
刊名	CURRENT BIOINFORMATICS
	2013-04-01
卷号	8 期号:2 页码:148-160
关键词	Coevolution analysis correlated mutation algorithms molecular dynamics simulation multiple sequence alignment phylogenetic bias phylogenetic correlation residue coevolution
英文摘要	Correlated mutation is regarded as a phenomenon induced by the demand of maintaining the structure and/or function of a protein during its biological evolution. Since it is closely related to the underlying mechanism of protein structure and function, tremendous efforts have been made to reveal the relationship between correlated mutations and the structure and function of the protein. In the past few decades, different coevolutionary analysis algorithms have been developed. They have been applied to study various aspects of protein structure and function, such as prediction of disulfide bonds, functionally important residues, residue-residue contacts and protein-protein interaction. Although considerable progress has been achieved so far, obstacles exist in many aspects such as identification, evaluation and interpretation of correlated mutations. In this review, we discuss several essential issues related to the overcoming of these obstacles in coevolution analysis, including the alignment size bias, phylogenetic bias, algorithm evaluation and coevolution interpretation. In particular, we focus on the inconsistent results generated by different algorithms and discuss possible reasons accounting for this discrepancy. We also discuss future challenges and research directions in coevolution analysis.
WOS标题词	Science & Technology ; Life Sciences & Biomedicine
类目[WOS]	Biochemical Research Methods ; Mathematical & Computational Biology
研究领域[WOS]	Biochemistry & Molecular Biology ; Mathematical & Computational Biology
关键词[WOS]	MULTIPLE SEQUENCE ALIGNMENTS ; INFORMATION-THEORETIC ANALYSIS ; MUTUAL INFORMATION ; COEVOLVING RESIDUES ; CONTACT PREDICTION ; MOLECULAR-DYNAMICS ; EVOLUTIONARY ; SITES ; IDENTIFICATION ; PHYLOGENY
收录类别	SCI
语种	英语
WOS记录号	WOS:000320466700003
内容类型	期刊论文
源URL	[http://124.16.173.210/handle/834782/1237]
专题	天津工业生物技术研究所_结构生物信息学和整合系统生物学实验室宋江宁_期刊论文
作者单位	1.Chinese Acad Sci, Key Lab Syst Microbial Biotechnol, Tianjin 300308, Peoples R China 2.Beijing Univ Technol, Sch Life Sci & Bioengn, Beijing 100124, Peoples R China 3.China Agr Univ, Coll Biol Sci, State Key Lab Agrobiotechnol, Beijing 100193, Peoples R China 4.Monash Univ, Dept Biochem & Mol Biol, Fac Med, Melbourne, Vic 3800, Australia
推荐引用方式 GB/T 7714	Xu, Haisong,Li, Xiaoqin,Zhang, Ziding,et al. Identifying Coevolution Between Amino Acid Residues in Protein Families: Advances in the Improvement and Evaluation of Correlated Mutation Algorithms[J]. CURRENT BIOINFORMATICS,2013,8(2):148-160.
APA	Xu, Haisong,Li, Xiaoqin,Zhang, Ziding,&Song, Jiangning.(2013).Identifying Coevolution Between Amino Acid Residues in Protein Families: Advances in the Improvement and Evaluation of Correlated Mutation Algorithms.CURRENT BIOINFORMATICS,8(2),148-160.
MLA	Xu, Haisong,et al."Identifying Coevolution Between Amino Acid Residues in Protein Families: Advances in the Improvement and Evaluation of Correlated Mutation Algorithms".CURRENT BIOINFORMATICS 8.2(2013):148-160.