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Paircoil2: improved prediction of coiled coils from sequence.

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McDonnell, A. V., Jiang, T., Keating, A. E., Berger, B.·2006·Bioinformatics

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Abstract

Summary: We introduce Paircoil2, a new version of the Paircoil program, which uses pairwise residue probabilities to detect coiled–coil motifs in protein sequence data. Paircoil2 achieves 98% sensitivity and 97% specificity on known coiled coils in leave-family-out cross-validation. It also shows superior performance compared with published methods in tests on proteins of known structure. Availability: Paircoil2 is freely available as a web application and for download at Contact: keating@mit.edu; bab@mit.edu Supplementary information: Available at Bioinformatics online and at the Paircoil website.

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Authors: McDonnell, A. V., Jiang, T., Keating, A. E., & Berger, B.
Affiliations: MIT Computer Science and Artificial Intelligence Laboratory (US)
Massachusetts Institute of Technology (US)
Corresponding author: Keating, A. E.
Berger, B.
ORCID: Jiang, T.
Keating, A. E.
Berger, B.
Venue: Bioinformatics
Publisher: Oxford University Press (OUP)
Published: 2005-11-29
Volume: 22
Issue: 3
Pages: 356-358
ISSN: 1367-4803 (ISSN-L)
1367-4811
DOI: 10.1093/bioinformatics/bti797
OpenAlex: W2117709367
Semantic Scholar: 67080275c2f525632c88cf8bec8612acc6963372
Cited by: 424
References: 22
Citations by year: 2026: 5 · 2025: 8 · 2024: 16 · 2023: 15 · 2022: 18 · 2021: 27 · 2020: 19 · 2019: 25 · 2018: 19 · 2017: 27 · 2016: 25 · 2015: 22 · 2014: 25 · 2013: 22 · 2012: 41
FWCI: 4.64
Type: journal article
Language: en
Open access: bronze
doi.org
Locations: Bioinformatics (publishedVersion)
PubMed (publishedVersion)
Funders: National Science Foundation (0347203, CAREER)
National Institutes of Health
National Institute of General Medical Sciences (GM67681, R01GM067681)
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
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords: coiled-coil domain, protein sequence analysis, web application, structure prediction
MeSH terms: Algorithms, Amino Acid Sequence, Computer Simulation, Models, Chemical, Models, Molecular, Molecular Sequence Data, Sensitivity and Specificity, Software, Reproducibility of Results, Sequence Analysis, Protein

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Paircoil2: improved prediction of coiled coils from sequence.

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