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PubMed · 6639935

Secondary structure assignment for alpha/beta proteins by a combinatorial approach.

F E Cohen·R M Abarbanel·I D Kuntz·R J Fletterick
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Abstract

We describe an algorithm for assigning the secondary structure of alpha/beta proteins. Turns are identified very accurately (98%) by simultaneously considering hydrophilicity and the ideal spacing of turns throughout the sequence. The segments bounded by these turns are labeled by a pattern-recognition scheme based on the physical properties of alpha-helices and beta-strands, in this class of proteins. Long-range, as well as local, information is incorporated to enhance the quality of the assignments. Although the assignment for any one sequence is not unique, at least one of the assignments bears a close resemblance to the native structure. The algorithm successfully divides protein sequences into two classes: alpha/beta and non-alpha/beta. The accuracy of the secondary-structure assignments in the alpha/beta class is sufficient to provide useful input for tertiary-structure assignments.

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IsomerismMacromolecular SubstancesMathematicsModels, MolecularProtein ConformationProteinsStructure-Activity RelationshipComparative StudyJournal ArticleResearch Support, Non-U.S. Gov'tResearch Support, U.S. Gov't, P.H.S.

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F E Cohen, R M Abarbanel, I D Kuntz, R J Fletterick. 1983-10-11. Secondary structure assignment for alpha/beta proteins by a combinatorial approach.. https://doi.org/10.1021/bi00290a005

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