Prediction of protein secondary structure with a reliability score estimated by local sequence clustering

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	Prediction of protein secondary structure with a reliability score estimated by local sequence clustering
	Jiang, F
刊名	PROTEIN ENGINEERING
	2003
卷号	16 期号:9 页码:651
关键词	NEURAL-NETWORKS GLOBULAR-PROTEINS ALIGNMENTS CLASSIFICATION IMPROVEMENT RECOGNITION 70-PERCENT DATABASE ACCURACY PROFILES
ISSN号	0269-2139
通讯作者	Jiang, F (reprint author), Chinese Acad Sci, Inst Phys, POB 603, Beijing 100080, Peoples R China.
中文摘要	Most algorithms for protein secondary structure prediction are based on machine learning techniques, e.g. neural networks. Good architectures and learning methods have improved the performance continuously. The introduction of profile methods, e.g. PSI-BLAST, has been a major breakthrough in increasing the prediction accuracy to close to 80%. In this paper, a brute-force algorithm is proposed and the reliability of each prediction is estimated by a z-score based on local sequence clustering. This algorithm is intended to perform well for those secondary structures in a protein whose formation is mainly dominated by the neighboring sequences and short-range interactions. A reliability z-score has been defined to estimate the goodness of a putative cluster found for a query sequence in a database. The database for prediction was constructed by experimentally determined, non-redundant protein structures with <25% sequence homology, a list maintained by PDBSELECT. Our test results have shown that this new algorithm, belonging to what is known as nearest neighbor methods, performed very well within the expectation of previous methods and that the reliability z-score as defined was correlated with the reliability of prediction. This led to the possibility of making very accurate predictions for a few selected residues in a protein with an accuracy measure of Q(3) > 80%. The further development of this algorithm, and a nucleation mechanism for protein folding are suggested.
收录类别	SCI
语种	英语
公开日期	2013-09-24
内容类型	期刊论文
源URL	[http://ir.iphy.ac.cn/handle/311004/51226]
专题	物理研究所_物理所公开发表论文_物理所公开发表论文_期刊论文
推荐引用方式 GB/T 7714	Jiang, F. Prediction of protein secondary structure with a reliability score estimated by local sequence clustering[J]. PROTEIN ENGINEERING,2003,16(9):651.
APA	Jiang, F.(2003).Prediction of protein secondary structure with a reliability score estimated by local sequence clustering.PROTEIN ENGINEERING,16(9),651.
MLA	Jiang, F."Prediction of protein secondary structure with a reliability score estimated by local sequence clustering".PROTEIN ENGINEERING 16.9(2003):651.