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SnapDRAGON: a method to delineate protein structural domains from sequence data.

Richard A George·Jaap Heringa
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Abstract

We describe a method to identify protein domain boundaries from sequence information alone based on the assumption that hydrophobic residues cluster together in space. SnapDRAGON is a suite of programs developed to predict domain boundaries based on the consistency observed in a set of alternative ab initio three-dimensional (3D) models generated for a given protein multiple sequence alignment. This is achieved by running a distance geometry-based folding technique in conjunction with a 3D-domain assignment algorithm. The overall accuracy of our method in predicting the number of domains for a non-redundant data set of 414 multiple alignments, representing 185 single and 231 multiple-domain proteins, is 72.4 %. Using domain linker regions observed in the tertiary structures associated with each query alignment as the standard of truth, inter-domain boundary positions are delineated with an accuracy of 63.9 % for proteins comprising continuous domains only, and 35.4 % for proteins with discontinuous domains. Overall, domain boundaries are delineated with an accuracy of 51.8 %. The prediction accuracy values are independent of the pair-wise sequence similarities within each of the alignments. These results demonstrate the capability of our method to delineate domains in protein sequences associated with a wide variety of structural domain organisation.

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AlgorithmsComputational BiologyDatabases, ProteinHydrophobic and Hydrophilic InteractionsModels, MolecularProtein FoldingProtein Structure, TertiaryProteinsReproducibility of ResultsSensitivity and SpecificitySequence AlignmentSequence AnalysisSoftwareStatistics as TopicJournal ArticleResearch Support, Non-U.S. Gov't

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BibTeXRIS

Richard A George, Jaap Heringa. 2002-02-22. SnapDRAGON: a method to delineate protein structural domains from sequence data.. https://doi.org/10.1006/jmbi.2001.5387

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