Protein Engineering, Vol. 13, No. 8, 535-543,
August 2000
© 2000 Oxford University Press
Protein structure alignment using environmental profiles
Laboratory of Molecular Biology, Division of Basic Sciences, National Cancer Institute, National Institutes of Health, 37 Convent Drive, MSC 4255, Bethesda, MD 20892-4255, USA
A new protein structure alignment procedure is described. An initial alignment is made by comparing a one-dimensional list of primary, secondary and tertiary structural features (profiles) of two proteins, without explicitly considering the three-dimensional geometry of the structures. The alignment is then iteratively refined in the second step, in which new alignments are found by three-dimensional superposition of the structures based on the current alignment. This new procedure is fast enough to do all-against-all structural comparisons routinely. The procedure sometimes finds an alignment that suggests an evolutionary relationship and which is not normally obtained if only geometry is considered. All pair-wise comparisons were made among 3539 protein structural domains that represent all known protein structures. The resulting 3539 z-scores were used to cluster the proteins. The number of main clusters increased continuously as the z-cutoff was raised, but the number of multiple-member clusters showed a maximum at z-cutoff values of 5.0 and 5.5. When a z-cutoff value of 5.0 was used, the total number of main clusters was 2043, of which only 336 clusters had more than one member.
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