In:
Bioinformatics, Oxford University Press (OUP), Vol. 27, No. 14 ( 2011-07-15), p. 1908-1914
Abstract:
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. Availability: SCORER 2.0 is available via a web interface at http://coiledcoils.chm.bris.ac.uk/Scorer. Source code, training sets and Supporting Information can be downloaded from the same site. Contact: coiledcoils-scorer@sympa.bristol.ac.uk; d.n.woolfson@bristol.ac.uk Supplementary information:Supplementary data are available at Bioinformatics online.
Type of Medium:
Online Resource
ISSN:
1367-4803
,
1367-4811
DOI:
10.1093/bioinformatics/btr299
Language:
English
Publisher:
Oxford University Press (OUP)
Publication Date:
2011
detail.hit.zdb_id:
1468345-3
SSG:
12
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