Improved genetic algorithm-based protein structure comparisons: pairwise and multiple superpositions.
Three major improvements to a previously described method for automatic protein structure comparison are described. First, a limit to translations for the rigid-body superposition is now assigned according to the dimensions of the structures being compared. Second, examination of the effect of the gap penalty on the derivation of a sequence alignment corresponding to a given structure superposition has led to a method to evaluate alternative structure-based sequence alignments. Third, the pairwise procedure has been generalized to multiple structure alignment. This implementation of rigid-body superposition can recognize well documented distant relationships which hitherto have required consideration of additional features and properties as well as those relationships between proteins of different sizes. A much larger common scaffold or framework between six globins can be extracted than that obtained using a standard algorithm for multiple structure superposition.
May
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AC
Imperial Cancer Research Fund Unit of Structural Molecular Biology, Department of Crystallography, Birkbeck College, University of London, UK.
Johnson
M S
MS
D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D002147:Calmodulin / Q000737:chemistry; D003087:Colicins / Q000737:chemistry; D004330:Drosophila / Q000378:metabolism; D008969:Molecular Sequence Data; D009414:Nerve Growth Factors / Q000737:chemistry; D010798:Phycocyanin / Q000737:chemistry; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment; D012984:Software; D016212:Transforming Growth Factor beta / Q000737:chemistry
D002147:Calmodulin; D003087:Colicins; D009414:Nerve Growth Factors; D011506:Proteins; D016212:Transforming Growth Factor beta; D010798:Phycocyanin