SCORER 2.0: an algorithm for distinguishing parallel dimeric and trimeric coiled-coil sequences
Open accessAbstract
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.
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Initial attempts on predicting oligomerization states in coiled coils focused on distinguishing dimers from trimers.
“Initial attempts on predicting oligomerization states in coiled coils focused on distinguishing dimers from trimers.34−39”
From Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints (2025) · cites this paper as [35]
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- Authors
- Armstrong, C. T., Vincent, T. L., Green, P. J., & Woolfson, D. N.
- Affiliations
- University of Bristol (GB)
- ORCID
- Woolfson, Derek N.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2011-05-16
- Volume
- 27
- Issue
- 14
- Pages
- 1908-1914
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2109354682
- Cited by
- 49
- References
- 34
- Citations by year
- 2026: 2 · 2025: 3 · 2024: 1 · 2022: 2 · 2021: 3 · 2020: 1 · 2019: 2 · 2018: 2 · 2017: 4 · 2016: 2 · 2015: 5 · 2014: 7 · 2013: 6 · 2012: 8
- FWCI
- 2.86
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- Bristol Research (University of Bristol) (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- UTS ePRESS (University of Technology Sydney) (submittedVersion)
- Funders
- Engineering and Physical Sciences Research Council (EP/D063485/1)
- Biotechnology and Biological Sciences Research Council
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- coiled coil, parallel dimer, trimers, protein sequences, heptad repeat, protein-protein interaction, web server
- MeSH terms
- Algorithms, Proteins, Software, Protein Structure, Secondary, Internet, Sequence Analysis, Protein, Amino Acid Motifs, Protein Multimerization
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