{"id":"https://openalex.org/W3112182945","doi":"https://doi.org/10.1093/bioinformatics/btaa1041","title":"A library of coiled-coil domains: from regular bundles to peculiar twists","display_name":"A library of coiled-coil domains: from regular bundles to peculiar twists","publication_year":2020,"publication_date":"2020-12-01","ids":{"openalex":"https://openalex.org/W3112182945","doi":"https://doi.org/10.1093/bioinformatics/btaa1041","mag":"3112182945","pmid":"https://pubmed.ncbi.nlm.nih.gov/33325494"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa1041","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa1041","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/22-23/5368/36856077/btaa1041.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/22-23/5368/36856077/btaa1041.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103261715","display_name":"Krzysztof Szczepaniak","orcid":"https://orcid.org/0000-0002-6409-8348"},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Krzysztof Szczepaniak","raw_affiliation_strings":["Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw , 02-097 Warsaw, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw , 02-097 Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085370243","display_name":"Adriana Bukala","orcid":null},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Adriana Bukala","raw_affiliation_strings":["Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw , 02-097 Warsaw, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw , 02-097 Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065735814","display_name":"Ant\u00f4nio Marinho da Silva Neto","orcid":"https://orcid.org/0000-0001-6261-249X"},"institutions":[{"id":"https://openalex.org/I25112270","display_name":"Universidade Federal de Pernambuco","ror":"https://ror.org/047908t24","country_code":"BR","type":"education","lineage":["https://openalex.org/I25112270"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Antonio Marinho da Silva Neto","raw_affiliation_strings":["Molecular Prospecting and Bioinformatics Group, Laboratory of Immunopathology Keizo Asami, Federal University of Pernambuco , 50670-901 Recife, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Molecular Prospecting and Bioinformatics Group, Laboratory of Immunopathology Keizo Asami, Federal University of Pernambuco , 50670-901 Recife, Brazil","institution_ids":["https://openalex.org/I25112270"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070900612","display_name":"Jan Ludwiczak","orcid":"https://orcid.org/0000-0002-3487-5433"},"institutions":[{"id":"https://openalex.org/I16778253","display_name":"Instytut Biologii Do\u015bwiadczalnej im. Marcelego Nenckiego","ror":"https://ror.org/04waf7p94","country_code":"PL","type":"facility","lineage":["https://openalex.org/I16778253","https://openalex.org/I99542240"]},{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Jan Ludwiczak","raw_affiliation_strings":["Laboratory of Bioinformatics, Nencki Institute of Experimental Biology , 02-093 Warsaw, Poland","Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw , 02-097 Warsaw, Poland"],"raw_orcid":"https://orcid.org/0000-0002-3487-5433","affiliations":[{"raw_affiliation_string":"Laboratory of Bioinformatics, Nencki Institute of Experimental Biology , 02-093 Warsaw, Poland","institution_ids":["https://openalex.org/I16778253"]},{"raw_affiliation_string":"Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw , 02-097 Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5072592637","display_name":"Stanis\u0142aw Dunin-Horkawicz","orcid":"https://orcid.org/0000-0002-4581-1558"},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Stanislaw Dunin-Horkawicz","raw_affiliation_strings":["Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw , 02-097 Warsaw, Poland"],"raw_orcid":"https://orcid.org/0000-0002-4581-1558","affiliations":[{"raw_affiliation_string":"Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw , 02-097 Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5072592637"],"corresponding_institution_ids":["https://openalex.org/I4654613"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.2503,"has_fulltext":false,"cited_by_count":34,"citation_normalized_percentile":{"value":0.7953189,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"36","issue":"22-23","first_page":"5368","last_page":"5376"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.13689999282360077,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.13689999282360077,"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/T10492","display_name":"Microtubule and mitosis dynamics","score":0.1216999962925911,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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/T11162","display_name":"Enzyme Structure and Function","score":0.10369999706745148,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/coiled-coil","display_name":"Coiled coil","score":0.7527627944946289},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4572437107563019},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.3518831133842468},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3440542221069336},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2544042468070984},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.09123939275741577}],"concepts":[{"id":"https://openalex.org/C55988834","wikidata":"https://www.wikidata.org/wiki/Q903650","display_name":"Coiled coil","level":2,"score":0.7527627944946289},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4572437107563019},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.3518831133842468},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3440542221069336},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2544042468070984},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.09123939275741577}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaa1041","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa1041","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/22-23/5368/36856077/btaa1041.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33325494","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33325494","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":null},{"id":"pmh:oai:pubmedcentral.nih.gov:8016460","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8016460","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa1041","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa1041","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/22-23/5368/36856077/btaa1041.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6076663254","display_name":null,"funder_award_id":"2019/32/T/NZ1/00323","funder_id":"https://openalex.org/F4320322511","funder_display_name":"Narodowe Centrum Nauki"},{"id":"https://openalex.org/G7616128522","display_name":null,"funder_award_id":"GA71-24","funder_id":"https://openalex.org/F4320323873","funder_display_name":"Uniwersytet Warszawski"},{"id":"https://openalex.org/G7896927281","display_name":null,"funder_award_id":"2015/18/E/ NZ1/00689","funder_id":"https://openalex.org/F4320322511","funder_display_name":"Narodowe Centrum Nauki"}],"funders":[{"id":"https://openalex.org/F4320322511","display_name":"Narodowe Centrum Nauki","ror":"https://ror.org/03ha2q922"},{"id":"https://openalex.org/F4320323873","display_name":"Uniwersytet Warszawski","ror":"https://ror.org/039bjqg32"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":40,"referenced_works":["https://openalex.org/W1717107635","https://openalex.org/W1961177618","https://openalex.org/W1987584191","https://openalex.org/W1988696168","https://openalex.org/W1993175766","https://openalex.org/W1997183226","https://openalex.org/W2005763580","https://openalex.org/W2008708467","https://openalex.org/W2008800209","https://openalex.org/W2014282792","https://openalex.org/W2017774235","https://openalex.org/W2019521315","https://openalex.org/W2030947664","https://openalex.org/W2031599624","https://openalex.org/W2032155561","https://openalex.org/W2036919668","https://openalex.org/W2068254342","https://openalex.org/W2072249997","https://openalex.org/W2077396167","https://openalex.org/W2109606373","https://openalex.org/W2116441099","https://openalex.org/W2152863678","https://openalex.org/W2170711116","https://openalex.org/W2261562349","https://openalex.org/W2292455539","https://openalex.org/W2538176089","https://openalex.org/W2565297360","https://openalex.org/W2575569425","https://openalex.org/W2579233876","https://openalex.org/W2747118545","https://openalex.org/W2763971786","https://openalex.org/W2778365038","https://openalex.org/W2802123268","https://openalex.org/W2810004940","https://openalex.org/W2895171702","https://openalex.org/W2903178267","https://openalex.org/W2907872701","https://openalex.org/W2951352852","https://openalex.org/W2952736989","https://openalex.org/W3146257408"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W4391375266","https://openalex.org/W1979597421","https://openalex.org/W2007980826","https://openalex.org/W2061531152","https://openalex.org/W3002753104","https://openalex.org/W2077600819","https://openalex.org/W2142036596","https://openalex.org/W2072657027"],"abstract_inverted_index":{"MOTIVATION:":[0],"Coiled":[1],"coils":[2,88,190],"are":[3,29,80,108,177,247],"widespread":[4],"protein":[5],"domains":[6],"involved":[7,191],"in":[8,82,181,192,202],"diverse":[9],"processes":[10],"ranging":[11],"from":[12],"providing":[13],"structural":[14,186],"rigidity":[15],"to":[16,34,41],"the":[17,54,62,71,74,84,113,203,228,231],"transduction":[18],"of":[19,57,66,70,86,93,105,131,146,170,175,188,207,230],"conformational":[20,195],"changes.":[21],"They":[22],"comprise":[23],"two":[24],"or":[25],"more":[26],"\u03b1-helices":[27],"that":[28],"wound":[30],"around":[31],"each":[32],"other":[33],"form":[35],"a":[36,124,143,217,223],"regular":[37],"supercoiled":[38],"bundle.":[39],"Owing":[40],"this":[42,94,119],"regularity,":[43],"coiled-coil":[44,149,162],"structures":[45,92,163],"can":[46,236],"be":[47,237],"described":[48],"with":[49,139],"parametric":[50],"equations,":[51],"thus":[52],"enabling":[53],"numerical":[55],"representation":[56],"their":[58],"properties,":[59],"such":[60,100],"as":[61,158,160,216,222],"degree":[63],"and":[64,73,89,107,205,221,239],"handedness":[65],"supercoiling,":[67],"rotational":[68],"state":[69],"helices,":[72],"offset":[75],"between":[76],"them.":[77],"These":[78],"descriptors":[79],"invaluable":[81],"understanding":[83],"function":[85],"coiled":[87,132,189,208],"designing":[90],"new":[91],"type.":[95],"The":[96,172],"existing":[97],"tools":[98],"for":[99,112,126],"calculations":[101],"require":[102],"manual":[103],"preparation":[104],"input":[106],"therefore":[109],"not":[110],"suitable":[111],"high-throughput":[114],"analyses.":[115],"RESULTS:":[116],"To":[117],"address":[118],"problem,":[120],"we":[121,141,183,198],"developed":[122],"SamCC-Turbo,":[123,140],"software":[125],"fully":[127],"automated,":[128],"per-residue":[129],"measurement":[130],"coils.":[133,209],"By":[134],"surveying":[135],"Protein":[136,232],"Data":[137,233],"Bank":[138,234],"generated":[142],"comprehensive":[144],"atlas":[145],"\u223c50":[147],"000":[148],"regions.":[150],"This":[151],"machine":[152],"learning-ready":[153],"dataset":[154],"features":[155,187],"precise":[156],"measurements":[157],"well":[159],"decomposes":[161],"into":[164],"fragments":[165],"characterized":[166],"by":[167,179],"various":[168],"degrees":[169],"supercoiling.":[171],"potential":[173],"applications":[174],"SamCC-Turbo":[176,213],"exemplified":[178],"analyses":[180],"which":[182],"reveal":[184],"general":[185],"functions":[193],"requiring":[194],"plasticity.":[196],"Finally,":[197],"discuss":[199],"further":[200],"directions":[201],"prediction":[204],"modeling":[206],"AVAILABILITY":[210],"AND":[211],"IMPLEMENTATION:":[212],"is":[214],"available":[215,248],"web":[218],"server":[219],"(https://lbs.cent.uw.edu.pl/samcc_turbo)":[220],"Python":[224],"library":[225],"(https://github.com/labstructbioinf/samcc_turbo),":[226],"whereas":[227],"results":[229],"scan":[235],"browsed":[238],"downloaded":[240],"at":[241,249],"https://lbs.cent.uw.edu.pl/ccdb.":[242],"SUPPLEMENTARY":[243],"INFORMATION:":[244],"Supplementary":[245],"data":[246],"Bioinformatics":[250],"online.":[251]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
