{"id":"https://openalex.org/W2254904118","doi":"https://doi.org/10.1093/bib/bbv047","title":"Critical evaluation ofin silicomethods for prediction of coiled-coil domains in proteins","display_name":"Critical evaluation ofin silicomethods for prediction of coiled-coil domains in proteins","publication_year":2015,"publication_date":"2015-07-15","ids":{"openalex":"https://openalex.org/W2254904118","doi":"https://doi.org/10.1093/bib/bbv047","mag":"2254904118","pmid":"https://pubmed.ncbi.nlm.nih.gov/26177815"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbv047","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbv047","pdf_url":"https://academic.oup.com/bib/article-pdf/17/2/270/25416651/bbv047.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in 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/bib/article-pdf/17/2/270/25416651/bbv047.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100369818","display_name":"Chen Li","orcid":"https://orcid.org/0000-0002-1847-754X"},"institutions":[{"id":"https://openalex.org/I37802460","display_name":"Northwest University","ror":"https://ror.org/00z3td547","country_code":"CN","type":"education","lineage":["https://openalex.org/I37802460"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chen Li","raw_affiliation_strings":["Chen Li received his M.Eng. in Computer Science from Northwest A&F University, China. He is currently pursuing his PhD in the Department of Biochemistry and Molecular Biology, Faculty of Medicine, Monash University. His research interests are structural bioinformatics, systems biology, data mining and machine learning","Biochemistry & Molecular Biology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chen Li received his M.Eng. in Computer Science from Northwest A&F University, China. He is currently pursuing his PhD in the Department of Biochemistry and Molecular Biology, Faculty of Medicine, Monash University. His research interests are structural bioinformatics, systems biology, data mining and machine learning","institution_ids":["https://openalex.org/I37802460"]},{"raw_affiliation_string":"Biochemistry & Molecular Biology","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060643624","display_name":"Catherine Ching Han Chang","orcid":null},"institutions":[{"id":"https://openalex.org/I11662577","display_name":"Monash University Malaysia","ror":"https://ror.org/00yncr324","country_code":"MY","type":"education","lineage":["https://openalex.org/I11662577","https://openalex.org/I56590836"]}],"countries":["MY"],"is_corresponding":false,"raw_author_name":"Catherine Ching Han Chang","raw_affiliation_strings":["Catherine Ching Han Chang received her degree in Chemical Engineering from Monash University Sunway Campus. She is currently pursuing PhD in Chemical Engineering in the Chemical Engineering Discipline, School of Engineering, Monash University, Malaysia. Her research interests include modelling of soluble recombinant protein expression in Escherichia coli"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Catherine Ching Han Chang received her degree in Chemical Engineering from Monash University Sunway Campus. She is currently pursuing PhD in Chemical Engineering in the Chemical Engineering Discipline, School of Engineering, Monash University, Malaysia. Her research interests include modelling of soluble recombinant protein expression in Escherichia coli","institution_ids":["https://openalex.org/I11662577"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021219848","display_name":"Jeremy Nagel","orcid":null},"institutions":[{"id":"https://openalex.org/I880331042","display_name":"Exelis (United States)","ror":"https://ror.org/011rxtm45","country_code":"US","type":"company","lineage":["https://openalex.org/I880331042"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeremy Nagel","raw_affiliation_strings":["Jeremy Nagel received his Bachelor in Environmental Science (Honours) from Monash University in 2011","Biochemistry & Molecular Biology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Jeremy Nagel received his Bachelor in Environmental Science (Honours) from Monash University in 2011","institution_ids":["https://openalex.org/I880331042"]},{"raw_affiliation_string":"Biochemistry & Molecular Biology","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042881187","display_name":"Benjamin T. Porebski","orcid":"https://orcid.org/0000-0003-1398-0442"},"institutions":[{"id":"https://openalex.org/I4210139041","display_name":"ARC Centre of Excellence for Innovations in Peptide and Protein Science","ror":"https://ror.org/04dxv8v14","country_code":"AU","type":"facility","lineage":["https://openalex.org/I1337719021","https://openalex.org/I165143802","https://openalex.org/I2801453606","https://openalex.org/I4210132349","https://openalex.org/I4210139041"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Benjamin T. Porebski","raw_affiliation_strings":["Benjamin T. Porebski received a BSc (Honours) in biochemistry and molecular biology from Monash University and is presently pursing a PhD in biochemistry in the Department of Biochemistry and Molecular Biology, Monash University, Australia. His research interests involve protein engineering using a wide spectrum of techniques including biophysics, protein crystallography and computational biology","Biochemistry & Molecular Biology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Benjamin T. Porebski received a BSc (Honours) in biochemistry and molecular biology from Monash University and is presently pursing a PhD in biochemistry in the Department of Biochemistry and Molecular Biology, Monash University, Australia. His research interests involve protein engineering using a wide spectrum of techniques including biophysics, protein crystallography and computational biology","institution_ids":["https://openalex.org/I4210139041"]},{"raw_affiliation_string":"Biochemistry & Molecular Biology","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039138118","display_name":"Morihiro Hayashida","orcid":"https://orcid.org/0000-0001-7961-0175"},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Morihiro Hayashida","raw_affiliation_strings":["Morihiro Hayashida received his PhD degree in Informatics in 2005 from Kyoto University, Japan. He is an assistant professor in Bioinformatics Center, Institute for Chemical Research, Kyoto University, Japan. His research interests include functional analysis of proteins and development of computational methods"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Morihiro Hayashida received his PhD degree in Informatics in 2005 from Kyoto University, Japan. He is an assistant professor in Bioinformatics Center, Institute for Chemical Research, Kyoto University, Japan. His research interests include functional analysis of proteins and development of computational methods","institution_ids":["https://openalex.org/I22299242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016330265","display_name":"Tatsuya Akutsu","orcid":"https://orcid.org/0000-0001-9763-797X"},"institutions":[{"id":"https://openalex.org/I4210148697","display_name":"Institute of Bioinformatics","ror":"https://ror.org/04hqfvm50","country_code":"IN","type":"nonprofit","lineage":["https://openalex.org/I4210148697"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Tatsuya Akutsu","raw_affiliation_strings":["Tatsuya Akutsu received his Dr. Eng. degree in Information Engineering in 1989 from University of Tokyo, Japan. Since 2001, he has been a professor in Bioinformatics Center, Institute for Chemical Research, Kyoto University, Japan. His research interests include bioinformatics and discrete algorithms"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tatsuya Akutsu received his Dr. Eng. degree in Information Engineering in 1989 from University of Tokyo, Japan. Since 2001, he has been a professor in Bioinformatics Center, Institute for Chemical Research, Kyoto University, Japan. His research interests include bioinformatics and discrete algorithms","institution_ids":["https://openalex.org/I4210148697"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012709797","display_name":"Jiangning Song","orcid":"https://orcid.org/0000-0001-8031-9086"},"institutions":[{"id":"https://openalex.org/I347366330","display_name":"Melbourne Bioinformatics","ror":"https://ror.org/05gkzhv48","country_code":"AU","type":"education","lineage":["https://openalex.org/I347366330"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Jiangning Song","raw_affiliation_strings":["Jiangning Song received his PhD degree in Bioinformatics in 2005 from Jiangnan University Wuxi China. He is a senior research fellow at the Monash Bioinformatics Platform, Faculty of Medicine, Monash University, Australia. He is also a principal investigator at the Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences. His research interests are bioinformatics, systems biology, machine learning, systems pharmacology and enzyme engineering","Biochemistry & Molecular Biology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Jiangning Song received his PhD degree in Bioinformatics in 2005 from Jiangnan University Wuxi China. He is a senior research fellow at the Monash Bioinformatics Platform, Faculty of Medicine, Monash University, Australia. He is also a principal investigator at the Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences. His research interests are bioinformatics, systems biology, machine learning, systems pharmacology and enzyme engineering","institution_ids":["https://openalex.org/I347366330"]},{"raw_affiliation_string":"Biochemistry & Molecular Biology","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5031275115","display_name":"Ashley M. Buckle","orcid":"https://orcid.org/0000-0003-2943-9044"},"institutions":[{"id":"https://openalex.org/I170203145","display_name":"MRC Laboratory of Molecular Biology","ror":"https://ror.org/00tw3jy02","country_code":"GB","type":"facility","lineage":["https://openalex.org/I170203145","https://openalex.org/I4210087105","https://openalex.org/I90344618"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Ashley M. Buckle","raw_affiliation_strings":["Ashley M Buckle completed his PhD in Biochemistry in 1994 in the laboratory of Prof. Sir Alan Fersht at the University of Cambridge, UK. He is an NHMRC senior research fellow and group leader in the Department of Biochemistry and Molecular Biology, Monash University, Australia. His laboratory uses a multidisciplinary approach to understand protein structure, dynamics and function, using protein crystallography, biophysics and molecular simulation","Biochemistry & Molecular Biology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ashley M Buckle completed his PhD in Biochemistry in 1994 in the laboratory of Prof. Sir Alan Fersht at the University of Cambridge, UK. He is an NHMRC senior research fellow and group leader in the Department of Biochemistry and Molecular Biology, Monash University, Australia. His laboratory uses a multidisciplinary approach to understand protein structure, dynamics and function, using protein crystallography, biophysics and molecular simulation","institution_ids":["https://openalex.org/I170203145"]},{"raw_affiliation_string":"Biochemistry & Molecular Biology","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":7,"institutions_distinct_count":8,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3885,"currency":"USD","value_usd":3885},"apc_paid":null,"fwci":1.1101,"has_fulltext":true,"cited_by_count":28,"citation_normalized_percentile":{"value":0.77669151,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"17","issue":"2","first_page":"270","last_page":"282"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9993000030517578,"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":0.9993000030517578,"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/T10604","display_name":"RNA Research and Splicing","score":0.9986000061035156,"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/T10949","display_name":"Genetic Neurodegenerative Diseases","score":0.9980999827384949,"subfield":{"id":"https://openalex.org/subfields/2804","display_name":"Cellular and Molecular Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/coiled-coil","display_name":"Coiled coil","score":0.8342622518539429},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6006187200546265},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5854272842407227},{"id":"https://openalex.org/keywords/uniprot","display_name":"UniProt","score":0.5509138703346252},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.47899100184440613},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.46247923374176025},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.4286336898803711},{"id":"https://openalex.org/keywords/structural-bioinformatics","display_name":"Structural bioinformatics","score":0.4231695830821991},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.40500950813293457},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37500816583633423},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.36758682131767273},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3626953959465027},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.357472687959671},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24479857087135315},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.18617510795593262},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1499461531639099}],"concepts":[{"id":"https://openalex.org/C55988834","wikidata":"https://www.wikidata.org/wiki/Q903650","display_name":"Coiled coil","level":2,"score":0.8342622518539429},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6006187200546265},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5854272842407227},{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.5509138703346252},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.47899100184440613},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.46247923374176025},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.4286336898803711},{"id":"https://openalex.org/C69131567","wikidata":"https://www.wikidata.org/wiki/Q2068215","display_name":"Structural bioinformatics","level":3,"score":0.4231695830821991},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.40500950813293457},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37500816583633423},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.36758682131767273},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3626953959465027},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.357472687959671},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24479857087135315},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.18617510795593262},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1499461531639099}],"mesh":[{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019281","descriptor_name":"Dimerization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019281","descriptor_name":"Dimerization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019281","descriptor_name":"Dimerization","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":4,"locations":[{"id":"doi:10.1093/bib/bbv047","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbv047","pdf_url":"https://academic.oup.com/bib/article-pdf/17/2/270/25416651/bbv047.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26177815","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26177815","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":"Briefings in bioinformatics","raw_type":"Comparative Study"},{"id":"pmh:oai:europepmc.org:5032797","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6078162","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:open-archive.highwire.org:bib:17/2/270","is_oa":false,"landing_page_url":"http://bib.oxfordjournals.org/cgi/content/short/17/2/270","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bib/bbv047","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbv047","pdf_url":"https://academic.oup.com/bib/article-pdf/17/2/270/25416651/bbv047.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.6200000047683716}],"awards":[{"id":"https://openalex.org/G1459452039","display_name":"Probability theory and statistics on a noncommutative topological monoid of strings and their application to bioremediation","funder_award_id":"16KT0020","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G1968171775","display_name":"Research Fellowship","funder_award_id":"1022688","funder_id":"https://openalex.org/F4320334705","funder_display_name":"National Health and Medical Research Council"},{"id":"https://openalex.org/G363136793","display_name":null,"funder_award_id":"R01 AI111990","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G4143271407","display_name":null,"funder_award_id":"AI111990","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G7341139379","display_name":"An Approach to Novel Structure Design by Combining Discrete Methods and Statistical Methods","funder_award_id":"26240034","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320320971","display_name":"Monash University","ror":"https://ror.org/02bfwt286"},{"id":"https://openalex.org/F4320321133","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35"},{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320334705","display_name":"National Health and Medical Research Council","ror":"https://ror.org/011kf5r70"},{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2254904118.pdf","grobid_xml":"https://content.openalex.org/works/W2254904118.grobid-xml"},"referenced_works_count":87,"referenced_works":["https://openalex.org/W341336861","https://openalex.org/W1577024459","https://openalex.org/W1766594731","https://openalex.org/W1965231243","https://openalex.org/W1967302489","https://openalex.org/W1971047357","https://openalex.org/W1978763290","https://openalex.org/W1982005006","https://openalex.org/W1982251004","https://openalex.org/W1983869242","https://openalex.org/W1984711666","https://openalex.org/W1985514943","https://openalex.org/W1987584191","https://openalex.org/W1989619236","https://openalex.org/W1993061512","https://openalex.org/W1994947657","https://openalex.org/W1998130142","https://openalex.org/W1998377570","https://openalex.org/W2002844124","https://openalex.org/W2006617902","https://openalex.org/W2010822247","https://openalex.org/W2015546050","https://openalex.org/W2016332933","https://openalex.org/W2017780934","https://openalex.org/W2017976446","https://openalex.org/W2023555945","https://openalex.org/W2027594237","https://openalex.org/W2032155561","https://openalex.org/W2034930832","https://openalex.org/W2037169923","https://openalex.org/W2040818153","https://openalex.org/W2046132401","https://openalex.org/W2046371018","https://openalex.org/W2051370951","https://openalex.org/W2051503991","https://openalex.org/W2052883021","https://openalex.org/W2053224153","https://openalex.org/W2058062660","https://openalex.org/W2059179327","https://openalex.org/W2064551580","https://openalex.org/W2069470894","https://openalex.org/W2070121169","https://openalex.org/W2072591681","https://openalex.org/W2073012734","https://openalex.org/W2075644998","https://openalex.org/W2076089035","https://openalex.org/W2083774304","https://openalex.org/W2092954353","https://openalex.org/W2098742973","https://openalex.org/W2102687634","https://openalex.org/W2103964575","https://openalex.org/W2109354682","https://openalex.org/W2113120594","https://openalex.org/W2115114820","https://openalex.org/W2115396351","https://openalex.org/W2117709367","https://openalex.org/W2117996955","https://openalex.org/W2118372625","https://openalex.org/W2119336981","https://openalex.org/W2119821739","https://openalex.org/W2122210511","https://openalex.org/W2125358782","https://openalex.org/W2125531604","https://openalex.org/W2128653811","https://openalex.org/W2129507204","https://openalex.org/W2129508689","https://openalex.org/W2130471829","https://openalex.org/W2137924550","https://openalex.org/W2138906106","https://openalex.org/W2140112946","https://openalex.org/W2152911717","https://openalex.org/W2153420734","https://openalex.org/W2158714788","https://openalex.org/W2161072217","https://openalex.org/W2162085776","https://openalex.org/W2162993917","https://openalex.org/W2169482727","https://openalex.org/W2170456357","https://openalex.org/W2170747616","https://openalex.org/W2172219847","https://openalex.org/W2328496340","https://openalex.org/W2911964244","https://openalex.org/W4239510810","https://openalex.org/W4243228481","https://openalex.org/W6611553314","https://openalex.org/W6665065844","https://openalex.org/W6684830297"],"related_works":["https://openalex.org/W4214882023","https://openalex.org/W4383473016","https://openalex.org/W2039679484","https://openalex.org/W1564749278","https://openalex.org/W1433532214","https://openalex.org/W1885320193","https://openalex.org/W2136856901","https://openalex.org/W2557251634","https://openalex.org/W2181530468","https://openalex.org/W3177828909"],"abstract_inverted_index":{"Coiled-coils":[0],"refer":[1],"to":[2,60,172,182],"a":[3,12,37,135],"bundle":[4],"of":[5,11,21,24,46,52,67,110,138],"helices":[6],"coiled":[7],"together":[8],"like":[9],"strands":[10],"rope.":[13],"It":[14],"has":[15],"been":[16,58],"estimated":[17],"that":[18,34,192],"nearly":[19],"3%":[20],"protein-encoding":[22],"regions":[23],"genes":[25],"harbour":[26],"coiled-coil":[27,85,95,98,222],"domains":[28,179],"(CCDs).":[29],"Experimental":[30],"studies":[31],"have":[32,57],"confirmed":[33,171],"CCDs":[35,68,147,157,174],"play":[36],"fundamental":[38],"role":[39],"in":[40,69,108,208,217],"subcellular":[41],"infrastructure":[42],"and":[43,64,76,82,97,104,118,145,148,211,223],"controlling":[44],"trafficking":[45],"eukaryotic":[47],"cells.":[48],"Given":[49],"the":[50,62,122],"importance":[51],"coiled-coils,":[53],"multiple":[54],"bioinformatics":[55,80,209],"tools":[56,83],"developed":[59],"facilitate":[61],"systematic":[63],"high-throughput":[65],"prediction":[66,114],"proteins.":[70],"In":[71,131],"this":[72,193],"article,":[73],"we":[74,133],"review":[75],"compare":[77],"12":[78],"sequence-based":[79],"approaches":[81,88,220],"for":[84,156,201,212,221],"prediction.":[86,101,189,227],"These":[87],"can":[89],"be":[90,173,197],"categorized":[91],"into":[92],"two":[93,165,168],"classes:":[94],"detection":[96],"oligomeric":[99,149,187,225],"state":[100,188,226],"We":[102,190],"evaluated":[103],"compared":[105],"these":[106],"methods":[107,117],"terms":[109],"their":[111],"input/output,":[112],"algorithm,":[113],"performance,":[115],"validation":[116],"software":[119],"utility.":[120],"All":[121],"independent":[123],"testing":[124],"data":[125],"sets":[126],"are":[127,215],"available":[128],"at":[129],"http://lightning.med.monash.edu/coiledcoil/.":[130],"addition,":[132],"conducted":[134],"case":[136],"study":[137],"nine":[139],"human":[140],"polyglutamine":[141],"(PolyQ)":[142],"disease-related":[143],"proteins":[144,169],"predicted":[146,181],"states":[150],"using":[151,186],"various":[152],"predictors.":[153,163],"Prediction":[154],"results":[155],"were":[158,170,180],"highly":[159],"variable":[160],"among":[161],"different":[162],"Only":[164],"peptides":[166],"from":[167],"by":[175],"majority":[176],"voting.":[177],"Both":[178],"form":[183],"dimeric":[184],"coiled-coils":[185],"anticipate":[191],"comprehensive":[194],"analysis":[195],"will":[196],"an":[198],"insightful":[199],"resource":[200],"structural":[202],"biologists":[203],"with":[204],"limited":[205],"prior":[206],"experience":[207],"tools,":[210],"bioinformaticians":[213],"who":[214],"interested":[216],"designing":[218],"novel":[219],"its":[224]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":1}],"updated_date":"2026-08-27T14:10:00.468798","created_date":"2016-06-24T00:00:00"}