MINRMS: an efficient algorithm for determining protein structure similarity using root-mean-squared-distance

被引:41
作者
Jewett, AI [1 ]
Huang, CC [1 ]
Ferrin, TE [1 ]
机构
[1] Univ Calif San Francisco, Dept Pharmaceut Chem, Comp Graph Lab, San Francisco, CA 94143 USA
关键词
D O I
10.1093/bioinformatics/btg035
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Motivation: Existing algorithms for automated protein structure alignment generate contradictory results and are difficult to interpret. An algorithm which can provide a context for interpreting the alignment and uses a simple method to characterize protein structure similarity is needed. Results: We describe a heuristic for limiting the search space for structure alignment comparisons between two proteins, and an algorithm for finding minimal root-mean-squared-distance (RMSD) alignments as a function of the number of matching residue pairs within this limited search space. Our alignment algorithm uses coordinates of alpha-carbon atoms to represent each amino acid residue and requires a total computation time of O (m(3)n(2)), where m and n denote the lengths of the protein sequences. This makes our method fast enough for comparisons of moderate-size proteins (fewer than similar to800 residues) on current workstation-class computers and therefore addresses the need for a systematic analysis of multiple plausible shape similarities between two proteins using a widely accepted comparison metric.
引用
收藏
页码:625 / 634
页数:10
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