DOI: 10.1093/bioinformatics/btr299. SCORER 2.0: an algorithm for distinguishing parallel dimeric and trimeric coiled-coil sequences

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

10.1093/bioinformatics/btr299

Crossref journal-article

Oxford University Press (OUP)

Bioinformatics (286)

Abstract

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.

Bibliography

Armstrong, C. T., Vincent, T. L., Green, P. J., & Woolfson, D. N. (2011). SCORER 2.0: an algorithm for distinguishing parallel dimeric and trimeric coiled-coil sequences. Bioinformatics, 27(14), 1908â1914.

Authors 4

Craig T. Armstrong (first)
Thomas L. Vincent (additional)
Peter J. Green (additional)
Derek N. Woolfson (additional)

References 34 Referenced 42

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Dates

Type	When
Created	14 years, 3 months ago (May 16, 2011, 11:25 p.m.)
Deposited	2 years, 7 months ago (Jan. 27, 2023, 8:38 a.m.)
Indexed	3 weeks, 2 days ago (Aug. 5, 2025, 8:33 a.m.)
Issued	14 years, 3 months ago (May 16, 2011)
Published	14 years, 3 months ago (May 16, 2011)
Published Online	14 years, 3 months ago (May 16, 2011)
Published Print	14 years, 1 month ago (July 15, 2011)

Funders 0

None

BibTeX

@article{Armstrong_2011, title={SCORER 2.0: an algorithm for distinguishing parallel dimeric and trimeric coiled-coil sequences}, volume={27}, ISSN={1367-4811}, url={http://dx.doi.org/10.1093/bioinformatics/btr299}, DOI={10.1093/bioinformatics/btr299}, number={14}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Armstrong, Craig T. and Vincent, Thomas L. and Green, Peter J. and Woolfson, Derek N.}, year={2011}, month=may, pages={1908–1914} }

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  "abstract": "<jats:title>Abstract</jats:title>\n               <jats:p>Motivation: The coiled coil is a ubiquitous \u03b1-helical protein structure domain that directs and facilitates protein\u2013protein 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.</jats:p>\n               <jats:p>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.</jats:p>\n               <jats:p>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.</jats:p>\n               <jats:p>Contact: \u00a0coiledcoils-scorer@sympa.bristol.ac.uk; d.n.woolfson@bristol.ac.uk</jats:p>\n               <jats:p>Supplementary information:Supplementary data are available at Bioinformatics online.</jats:p>",
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