{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,21]],"date-time":"2026-01-21T05:55:59Z","timestamp":1768974959303,"version":"3.49.0"},"reference-count":52,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,1,1]]},"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, the coiled coil is readily recognized via a conspicuous heptad repeat of hydrophobic and polar residues. However, structurally coiled coils are more complicated, existing in a wide range of oligomer states and topologies. As a consequence, predicting these various states from sequence remains an unmet challenge.<\/jats:p>\n               <jats:p>Results: This work introduces LOGICOIL, the first algorithm to address the problem of predicting multiple coiled-coil oligomeric states from protein-sequence information alone. By covering &amp;gt;90% of the known coiled-coil structures, LOGICOIL is a net improvement compared with other existing methods, which achieve a predictive coverage of \u223c31% of this population. This leap in predictive power offers better opportunities for genome-scale analysis, and analyses of coiled-coil containing protein assemblies.<\/jats:p>\n               <jats:p>Availability: LOGICOIL is available via a web-interface at http:\/\/coiledcoils.chm.bris.ac.uk\/LOGICOIL. Source code, training sets and supporting information can be downloaded from the same site.<\/jats:p>\n               <jats:p>Contact: \u00a0D.N.Woolfson@bristol.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts648","type":"journal-article","created":{"date-parts":[[2012,11,6]],"date-time":"2012-11-06T03:08:43Z","timestamp":1352171323000},"page":"69-76","source":"Crossref","is-referenced-by-count":96,"title":["LOGICOIL\u2014multi-state prediction of coiled-coil oligomeric state"],"prefix":"10.1093","volume":"29","author":[{"given":"Thomas L.","family":"Vincent","sequence":"first","affiliation":[{"name":"1 School of Chemistry, University of Bristol, Bristol BS8 1TS, 2Bristol Centre for Complexity Science, University of Bristol, Bristol BS8 1TR, 3School of Mathematics, University of Bristol, Bristol BS8 1TW and 4School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK"},{"name":"1 School of Chemistry, University of Bristol, Bristol BS8 1TS, 2Bristol Centre for Complexity Science, University of Bristol, Bristol BS8 1TR, 3School of Mathematics, University of Bristol, Bristol BS8 1TW and 4School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter J.","family":"Green","sequence":"additional","affiliation":[{"name":"1 School of Chemistry, University of Bristol, Bristol BS8 1TS, 2Bristol Centre for Complexity Science, University of Bristol, Bristol BS8 1TR, 3School of Mathematics, University of Bristol, Bristol BS8 1TW and 4School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Derek N.","family":"Woolfson","sequence":"additional","affiliation":[{"name":"1 School of Chemistry, University of Bristol, Bristol BS8 1TS, 2Bristol Centre for Complexity Science, University of Bristol, Bristol BS8 1TR, 3School of Mathematics, University of Bristol, Bristol BS8 1TW and 4School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK"},{"name":"1 School of Chemistry, University of Bristol, Bristol BS8 1TS, 2Bristol Centre for Complexity Science, University of Bristol, Bristol BS8 1TR, 3School of Mathematics, University of Bristol, Bristol BS8 1TW and 4School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2012,11,4]]},"reference":[{"key":"2023020303205309000_bts648-B1","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1093\/bioinformatics\/btp638","article-title":"Bayesian variable selection for disease classification using gene expression data","volume":"26","author":"Ai-Jun","year":"2010","journal-title":"Bioinformatics"},{"key":"2023020303205309000_bts648-B2","doi-asserted-by":"crossref","first-page":"6352","DOI":"10.1021\/bi002829w","article-title":"Buried polar residues in coiled-coil interfaces","volume":"40","author":"Akey","year":"2001","journal-title":"Biochemistry"},{"key":"2023020303205309000_bts648-B3","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1080\/01621459.1993.10476321","article-title":"Bayesian analysis of binary and polychotomous response data","volume":"88","author":"Albert","year":"1993","journal-title":"J. Am. Stat. Assoc."},{"key":"2023020303205309000_bts648-B4","doi-asserted-by":"crossref","first-page":"1908","DOI":"10.1093\/bioinformatics\/btr299","article-title":"SCORER 2.0: an algorithm for distinguishing parallel dimeric and trimeric coiled-coil sequences","volume":"27","author":"Armstrong","year":"2011","journal-title":"Bioinformatics"},{"key":"2023020303205309000_bts648-B5","doi-asserted-by":"crossref","first-page":"1711","DOI":"10.1093\/bioinformatics\/btp286","article-title":"penalizedSVM: a R-package for feature selection SVM classification","volume":"25","author":"Becker","year":"2009","journal-title":"Bioinformatics"},{"key":"2023020303205309000_bts648-B6","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2023020303205309000_bts648-B7","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1111\/1467-9868.00348","article-title":"Bayes model averaging with selection of regressors","volume":"64","author":"Brown","year":"2002","journal-title":"J. R. Stat. Soc. B"},{"key":"2023020303205309000_bts648-B8","doi-asserted-by":"crossref","first-page":"689","DOI":"10.1107\/S0365110X53001964","article-title":"The packing of \u03b1-helices\u2014simple coiled coils","volume":"6","author":"Crick","year":"1953","journal-title":"Acta Crystallogr."},{"key":"2023020303205309000_bts648-B9","doi-asserted-by":"crossref","first-page":"861","DOI":"10.1016\/j.patrec.2005.10.010","article-title":"An introduction to ROC analysis","volume":"27","author":"Fawcett","year":"2006","journal-title":"Pattern Recognit. Lett."},{"key":"2023020303205309000_bts648-B10","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1016\/S0304-4076(00)00076-2","article-title":"Benchmark priors for Bayesian model averaging","volume":"100","author":"Fernandez","year":"2001","journal-title":"J. Econom."},{"key":"2023020303205309000_bts648-B11","volume-title":"Bayesian Data Analysis","author":"Gelman","year":"2004","edition":"2nd"},{"key":"2023020303205309000_bts648-B12","doi-asserted-by":"crossref","first-page":"1011","DOI":"10.1038\/nsb1296-1011","article-title":"Buried polar residues and structural specificity in the GCN4 leucine-zipper","volume":"3","author":"Gonzalez","year":"1996","journal-title":"Nat. Struct. Biol."},{"key":"2023020303205309000_bts648-B13","doi-asserted-by":"crossref","first-page":"711","DOI":"10.1093\/biomet\/82.4.711","article-title":"Reversible jump Markov Chain Monte Carlo computation and Bayesian model determination","volume":"82","author":"Green","year":"1995","journal-title":"Biometrika"},{"key":"2023020303205309000_bts648-B14","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1016\/j.jsb.2006.03.009","article-title":"Comparative analysis of coiled-coil prediction methods","volume":"155","author":"Gruber","year":"2006","journal-title":"J. Struct. Biol."},{"key":"2023020303205309000_bts648-B15","doi-asserted-by":"crossref","first-page":"1478","DOI":"10.1214\/08-AOAS188","article-title":"Bayesian multinomial regression with class-specific predictor selection","volume":"2","author":"Gustafson","year":"2008","journal-title":"Ann. Appl. Stat."},{"key":"2023020303205309000_bts648-B16","doi-asserted-by":"crossref","first-page":"530","DOI":"10.1073\/pnas.0709068105","article-title":"Preferred side-chain costellations at antiparallel coiled-coil interfaces","volume":"105","author":"Hadley","year":"2008","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023020303205309000_bts648-B17","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1023\/A:1010920819831","article-title":"A simple generalisation of the area under the ROC curve for multiple class classification problem","volume":"45","author":"Hand","year":"2001","journal-title":"Mach. Learn."},{"key":"2023020303205309000_bts648-B18","doi-asserted-by":"crossref","first-page":"1401","DOI":"10.1126\/science.8248779","article-title":"A switch between two-, three-, and four-stranded coiled coils in GCN4 leucine zipper mutants","volume":"262","author":"Harbury","year":"1993","journal-title":"Science"},{"key":"2023020303205309000_bts648-B19","doi-asserted-by":"crossref","first-page":"16950","DOI":"10.1073\/pnas.0907256106","article-title":"A coiled-coil motif that sequesters ions to the hydrophobic core","volume":"106","author":"Hartmann","year":"2009","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023020303205309000_bts648-B20","doi-asserted-by":"crossref","first-page":"1471","DOI":"10.1162\/neco.2006.18.6.1472","article-title":"Support vector machines for dyadic data","volume":"18","author":"Hochreiter","year":"2006","journal-title":"Neural Comput."},{"key":"2023020303205309000_bts648-B21","first-page":"145","article-title":"Bayesian auxiliary variable models for binary and multinomial regression","volume":"1","author":"Holmes","year":"2006","journal-title":"Bayesian Anal."},{"key":"2023020303205309000_bts648-B22","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1016\/j.jeconom.2004.02.002","article-title":"A Bayesian analysis of the multinomial probit model using the marginal data augmentation","volume":"124","author":"Imai","year":"2005","journal-title":"J. Econom."},{"key":"2023020303205309000_bts648-B23","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v014.i03","article-title":"MNP: R package for fitting multinomial probit models","volume":"14","author":"Imai","year":"2005","journal-title":"J. Stat. Softw."},{"key":"2023020303205309000_bts648-B24","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1016\/S0968-0004(01)02039-4","article-title":"Getting the most from PSI-BLAST","volume":"27","author":"Jones","year":"2002","journal-title":"Trends Biochem. Sci."},{"key":"2023020303205309000_bts648-B25","doi-asserted-by":"crossref","first-page":"592","DOI":"10.1198\/jcgs.2009.08027","article-title":"Transdimensional sampling algorithms for Bayesian variable selection in classification problems with many more variables than observations","volume":"18","author":"Lamnisos","year":"2009","journal-title":"J. Comput. Graph. Stat."},{"key":"2023020303205309000_bts648-B26","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1007\/s11222-011-9228-1","article-title":"Cross-validation prior choice in Bayesian probit regression with many covariates","volume":"22","author":"Lamnisos","year":"2012","journal-title":"Stat. Comput."},{"key":"2023020303205309000_bts648-B27","doi-asserted-by":"crossref","first-page":"2947","DOI":"10.1093\/bioinformatics\/btm404","article-title":"CLUSTAL W and CLUSTAL X version 2.0","volume":"23","author":"Larkin","year":"2007","journal-title":"Bioinformatics"},{"key":"2023020303205309000_bts648-B28","doi-asserted-by":"crossref","first-page":"1658","DOI":"10.1093\/bioinformatics\/btl158","article-title":"CD-HIT: a fast program for clustering and comparing large sets of protein or nucleotide sequences","volume":"22","author":"Li","year":"2006","journal-title":"Bioinformatics"},{"key":"2023020303205309000_bts648-B29","first-page":"410","article-title":"Mixture of g-priors for Bayesian variable selection","volume":"103","author":"Liang","year":"2008","journal-title":"JAMA"},{"key":"2023020303205309000_bts648-B30","doi-asserted-by":"crossref","first-page":"168","DOI":"10.1016\/j.jmb.2006.05.063","article-title":"Conformational transition between four and five-stranded phenylalanine zippers determined by a local packing interaction","volume":"361","author":"Liu","year":"2006","journal-title":"J. Mol. Biol."},{"key":"2023020303205309000_bts648-B31","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/S0065-3233(05)70003-6","article-title":"The structure of \u03b1-helical coiled coils","volume":"70","author":"Lupas","year":"2005","journal-title":"Adv. Protein Chem."},{"key":"2023020303205309000_bts648-B32","doi-asserted-by":"crossref","DOI":"10.1074\/mcp.M110.004994","article-title":"Complex networks govern coiled-coil oligomerization\u2014predicting and profiling by means of a machine learning approach","volume":"10","author":"Mahrenholz","year":"2011","journal-title":"Mol. Cell Proteomics"},{"key":"2023020303205309000_bts648-B33","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4899-3242-6","volume-title":"Generalized Linear Models","author":"McCullagh","year":"1989"},{"key":"2023020303205309000_bts648-B34","doi-asserted-by":"crossref","first-page":"726","DOI":"10.1016\/j.jmb.2008.11.028","article-title":"A periodic table of coiled-coil protein structures","volume":"385","author":"Moutevelis","year":"2009","journal-title":"J. Mol. Biol."},{"key":"2023020303205309000_bts648-B35","first-page":"85","article-title":"A review of Bayesian variable selection methods: what, how and which","volume":"4","author":"O\u2019Hara","year":"2009","journal-title":"Bayesian Anal."},{"key":"2023020303205309000_bts648-B36","doi-asserted-by":"crossref","first-page":"480","DOI":"10.1016\/j.jmb.2010.08.032","article-title":"The evolution and structure prediction of coiled coils across all genomes","volume":"403","author":"Rackham","year":"2010","journal-title":"J. Mol. Biol."},{"key":"2023020303205309000_bts648-B37","doi-asserted-by":"crossref","first-page":"812","DOI":"10.1111\/j.0006-341X.2004.00233.x","article-title":"Bayesian variable selection in multinomial probit models to identify molecular signatures of disease stage","volume":"60","author":"Sha","year":"2004","journal-title":"Biometrics"},{"key":"2023020303205309000_bts648-B38","doi-asserted-by":"crossref","first-page":"3940","DOI":"10.1093\/bioinformatics\/bti623","article-title":"ROCR: visualizing classifier performance in R","volume":"21","author":"Sing","year":"2005","journal-title":"Bioinformatics"},{"key":"2023020303205309000_bts648-B39","doi-asserted-by":"crossref","first-page":"7586","DOI":"10.1021\/ja100080q","article-title":"Side-chain pairing preferences in the parallel coiled-coil dimer motif: insight on ion pairing between core and flanking sites","volume":"132","author":"Steinkruger","year":"2010","journal-title":"J. Am. Chem. Soc."},{"key":"2023020303205309000_bts648-B40","first-page":"659","article-title":"Bayesian models for variable selection that incorporate biological information","volume":"9","author":"Stingo","year":"2010","journal-title":"Bayesian Stat."},{"key":"2023020303205309000_bts648-B41","volume-title":"R: A Language and Environment for Statistical Computing","author":"Team","year":"1993"},{"key":"2023020303205309000_bts648-B42","doi-asserted-by":"crossref","first-page":"D315","DOI":"10.1093\/nar\/gkn675","article-title":"CC+: a relational database of coiled-coil structures","volume":"37","author":"Testa","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023020303205309000_bts648-B43","doi-asserted-by":"crossref","first-page":"e23519","DOI":"10.1371\/journal.pone.0023519","article-title":"Multicoil2: predicting coiled coils and their oligomerization states from sequence in the twilight zone","volume":"6","author":"Trigg","year":"2011","journal-title":"PLoS ONE"},{"key":"2023020303205309000_bts648-B44","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1198\/106186008X289849","article-title":"Bayesian variable selection for logistic models using auxiliary mixture sampling","volume":"17","author":"Tuchler","year":"2008","journal-title":"J. Comput. Graph. Stat."},{"key":"2023020303205309000_bts648-B45","doi-asserted-by":"crossref","first-page":"668","DOI":"10.1110\/ps.36901","article-title":"Open-and-shut cases in coiled-coil assembly: Alpha-sheets and alpha-cylinders","volume":"10","author":"Walshaw","year":"2001","journal-title":"Protein Sci."},{"key":"2023020303205309000_bts648-B46","doi-asserted-by":"crossref","first-page":"1427","DOI":"10.1006\/jmbi.2001.4545","article-title":"SOCKET: a program for identifying and analysing coiled-coil motifs within protein structures","volume":"307","author":"Walshaw","year":"2001","journal-title":"J. Mol. Biol."},{"key":"2023020303205309000_bts648-B47","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1016\/j.jsb.2003.10.014","article-title":"Extended knobs-into-holes packing in classical and complex coiled-coil assemblies","volume":"144","author":"Walshaw","year":"2003","journal-title":"J. Struct. Biol."},{"key":"2023020303205309000_bts648-B48","doi-asserted-by":"crossref","first-page":"1179","DOI":"10.1002\/pro.5560060606","article-title":"MultiCoil: a program for predicting two- and three-stranded coiled coils","volume":"6","author":"Wolf","year":"1997","journal-title":"Protein Sci."},{"key":"2023020303205309000_bts648-B49","doi-asserted-by":"crossref","first-page":"1596","DOI":"10.1002\/pro.5560040818","article-title":"Predicting oligomerization states of coiled coils","volume":"4","author":"Woolfson","year":"1995","journal-title":"Protein Sci."},{"key":"2023020303205309000_bts648-B50","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.1016\/S0169-409X(02)00058-3","article-title":"Coiled-coils: stability, specificity, and drug delivery potential","volume":"54","author":"Yu","year":"2002","journal-title":"Adv. Drug Deliv. Rev."},{"key":"2023020303205309000_bts648-B51","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1016\/j.jbi.2004.07.009","article-title":"Cancer classification and prediction using logistic regression with Bayesian gene selection","volume":"37","author":"Zhou","year":"2004","journal-title":"J. Biomed. Inform."},{"key":"2023020303205309000_bts648-B52","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1049\/ip-syb:20050015","article-title":"Multi-class cancer classification using multinomial probit regression with Bayesian gene selection","volume":"153","author":"Zhou","year":"2006","journal-title":"IEEE Proc. Syst. Biol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/1\/69\/49060611\/bioinformatics_29_1_69.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/1\/69\/49060611\/bioinformatics_29_1_69.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,3]],"date-time":"2023-02-03T03:23:03Z","timestamp":1675394583000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/29\/1\/69\/273113"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,11,4]]},"references-count":52,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2013,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts648","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,1]]},"published":{"date-parts":[[2012,11,4]]}}}