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Bioinformatics. 2003 Mar 22;19(5):625-34.

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

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Computer Graphics Laboratory, Department of Pharmaceutical Chemistry, University of California at San Fransisco, San Fransisco, CA 94143-0446, USA.



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.


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 approximately 800 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.

[Indexed for MEDLINE]

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