{"id":"https://openalex.org/W2117709367","doi":"https://doi.org/10.1093/bioinformatics/bti797","title":"Paircoil2: improved prediction of coiled coils from sequence","display_name":"Paircoil2: improved prediction of coiled coils from sequence","publication_year":2005,"publication_date":"2005-11-29","ids":{"openalex":"https://openalex.org/W2117709367","doi":"https://doi.org/10.1093/bioinformatics/bti797","mag":"2117709367","pmid":"https://pubmed.ncbi.nlm.nih.gov/16317077"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti797","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti797","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/3/356/587961/bti797.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/22/3/356/587961/bti797.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5029784517","display_name":"Andrew V. McDonnell","orcid":null},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"A. V. McDonnell","raw_affiliation_strings":["Mathematics Department, Computer Science and Artificial Intelligence Laboratory 1 \u00a0 1 \u00a0 \u00a0 Cambridge, MA 02139, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mathematics Department, Computer Science and Artificial Intelligence Laboratory 1 \u00a0 1 \u00a0 \u00a0 Cambridge, MA 02139, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062116814","display_name":"Taijiao Jiang","orcid":"https://orcid.org/0000-0002-6280-6347"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"T. Jiang","raw_affiliation_strings":["Department of Biology, Massachusetts Institute of Technology 2 \u00a0 2 \u00a0 \u00a0 Cambridge, MA 02139, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Massachusetts Institute of Technology 2 \u00a0 2 \u00a0 \u00a0 Cambridge, MA 02139, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068168068","display_name":"Amy E. Keating","orcid":"https://orcid.org/0000-0003-4074-8980"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"A. E. Keating","raw_affiliation_strings":["Department of Biology, Massachusetts Institute of Technology 2 \u00a0 2 \u00a0 \u00a0 Cambridge, MA 02139, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Massachusetts Institute of Technology 2 \u00a0 2 \u00a0 \u00a0 Cambridge, MA 02139, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044078921","display_name":"Bonnie Berger","orcid":"https://orcid.org/0000-0002-2724-7228"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"B. Berger","raw_affiliation_strings":["Mathematics Department, Computer Science and Artificial Intelligence Laboratory 1 \u00a0 1 \u00a0 \u00a0 Cambridge, MA 02139, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mathematics Department, Computer Science and Artificial Intelligence Laboratory 1 \u00a0 1 \u00a0 \u00a0 Cambridge, MA 02139, USA","institution_ids":["https://openalex.org/I63966007"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5044078921","https://openalex.org/A5068168068"],"corresponding_institution_ids":["https://openalex.org/I63966007"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":4.4215,"has_fulltext":true,"cited_by_count":451,"citation_normalized_percentile":{"value":0.95341093,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"22","issue":"3","first_page":"356","last_page":"358"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9987000226974487,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.7346327304840088},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6350902915000916},{"id":"https://openalex.org/keywords/coiled-coil","display_name":"Coiled coil","score":0.610181987285614},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5467033982276917},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.4715423882007599},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.44798922538757324},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.43271079659461975},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3653598427772522},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3323049247264862},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.28959691524505615},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.2833028733730316},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19801753759384155},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1481029987335205},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.06694865226745605}],"concepts":[{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.7346327304840088},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6350902915000916},{"id":"https://openalex.org/C55988834","wikidata":"https://www.wikidata.org/wiki/Q903650","display_name":"Coiled coil","level":2,"score":0.610181987285614},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5467033982276917},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.4715423882007599},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.44798922538757324},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.43271079659461975},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3653598427772522},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3323049247264862},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.28959691524505615},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.2833028733730316},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19801753759384155},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1481029987335205},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.06694865226745605},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bti797","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti797","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/3/356/587961/bti797.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:16317077","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16317077","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.106.201","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.106.201","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/cgi/reprint/22/3/356.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bti797","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti797","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/3/356/587961/bti797.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2609681874","display_name":"CAREER: Analysis of the Coiled-coil Interactome","funder_award_id":"0347203","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4932480804","display_name":null,"funder_award_id":"GM67681","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6671297155","display_name":null,"funder_award_id":"CAREER","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2117709367.pdf","grobid_xml":"https://content.openalex.org/works/W2117709367.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W1677326748","https://openalex.org/W1823814103","https://openalex.org/W1965231243","https://openalex.org/W1972449088","https://openalex.org/W1977074400","https://openalex.org/W1977845138","https://openalex.org/W1998130142","https://openalex.org/W2024645073","https://openalex.org/W2032155561","https://openalex.org/W2062926863","https://openalex.org/W2063742006","https://openalex.org/W2084290280","https://openalex.org/W2099432768","https://openalex.org/W2129508689","https://openalex.org/W2129567429","https://openalex.org/W2130472348","https://openalex.org/W2130479394","https://openalex.org/W2135083016","https://openalex.org/W2144983282","https://openalex.org/W2158714788","https://openalex.org/W2168211076","https://openalex.org/W4237410627"],"related_works":["https://openalex.org/W2194132979","https://openalex.org/W2018356890","https://openalex.org/W2051969447","https://openalex.org/W2111937814","https://openalex.org/W2162923930","https://openalex.org/W2113213844","https://openalex.org/W2129361631","https://openalex.org/W2079145549","https://openalex.org/W2903170547","https://openalex.org/W4389053053"],"abstract_inverted_index":{"Abstract":[0],"Summary:":[1],"We":[2],"introduce":[3],"Paircoil2,":[4],"a":[5,61],"new":[6],"version":[7],"of":[8,52],"the":[9,79],"Paircoil":[10,80],"program,":[11],"which":[12],"uses":[13],"pairwise":[14],"residue":[15],"probabilities":[16],"to":[17],"detect":[18],"coiled\u2013coil":[19],"motifs":[20],"in":[21,36,48],"protein":[22],"sequence":[23],"data.":[24],"Paircoil2":[25,56],"achieves":[26],"98%":[27],"sensitivity":[28],"and":[29,64,77],"97%":[30],"specificity":[31],"on":[32,50],"known":[33,53],"coiled":[34],"coils":[35],"leave-family-out":[37],"cross-validation.":[38],"It":[39],"also":[40],"shows":[41],"superior":[42],"performance":[43],"compared":[44],"with":[45],"published":[46],"methods":[47],"tests":[49],"proteins":[51],"structure.":[54],"Availability:":[55],"is":[57],"freely":[58],"available":[59],"as":[60],"web":[62],"application":[63],"for":[65],"download":[66],"at":[67,74,78],"Contact:":[68],"keating@mit.edu;":[69],"bab@mit.edu":[70],"Supplementary":[71],"information:":[72],"Available":[73],"Bioinformatics":[75],"online":[76],"website.":[81]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":18},{"year":2023,"cited_by_count":16},{"year":2022,"cited_by_count":22},{"year":2021,"cited_by_count":35},{"year":2020,"cited_by_count":27},{"year":2019,"cited_by_count":24},{"year":2018,"cited_by_count":20},{"year":2017,"cited_by_count":27},{"year":2016,"cited_by_count":26},{"year":2015,"cited_by_count":22},{"year":2014,"cited_by_count":25},{"year":2013,"cited_by_count":22},{"year":2012,"cited_by_count":42}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}
