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

CT Armstrong, TL Vincent, PJ Green, DN Woolfson

Research output: Contribution to journalArticle (Academic Journal)peer-review

35 Citations (Scopus)

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:
Translated title of the contributionSCORER 2.0: an algorithm for distinguishing parallel dimeric and trimeric coiled-coil sequences
Original languageEnglish
Pages (from-to)1908 - 1914
Number of pages7
JournalBioinformatics
Volume27 (14)
DOIs
Publication statusPublished - Jul 2011

Bibliographical note

Other: Original Paper

Fingerprint Dive into the research topics of 'SCORER 2.0: an algorithm for distinguishing parallel dimeric and trimeric coiled-coil sequences'. Together they form a unique fingerprint.

Cite this