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SCORER 2.0: An algorithm for distinguishing parallel dimeric and trimeric coiled-coil sequences

Bioinformatics, ISSN: 1367-4803, Vol: 27, Issue: 14, Page: 1908-1914
2011
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Article Description

Motivation: The coiled coil is a ubiquitous α-helical protein structure domain that directs and facilitates protein-protein interactions in a wide variety of biological processes. At the protein-sequence level, coiled coils are quite straightforward and readily recognized via the conspicuous heptad repeats of hydrophobic and polar residues. However, structurally they are more complicated, existing in a range of oligomer states and topologies. Here, we address the issue of predicting coiled-coil oligomeric state from protein sequence. Results: The predominant coiled-coil oligomer states in Nature are parallel dimers and trimers. Here, we improve and retrain the first-published algorithm, SCORER, that distinguishes these states, and test it against the current standard, MultiCoil. The SCORER algorithm has been revised in two key respects: first, the statistical basis for SCORER is improved markedly. Second, the training set for SCORER has been expanded and updated to include only structurally validated coiled coils. The result is a much-improved oligomer state predictor that outperforms MultiCoil, particularly in assigning oligomer state to short coiled coils, and those that are diverse from the training set. © The Author 2011. Published by Oxford University Press. All rights reserved.

Bibliographic Details

Craig T. Armstrong; Thomas L. Vincent; Derek N. Woolfson; Peter J. Green

Oxford University Press (OUP)

Mathematics; Biochemistry, Genetics and Molecular Biology; Computer Science

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