{"id":"https://openalex.org/W2003353954","doi":"https://doi.org/10.1093/nar/gkl264","title":"OPAAS: a web server for optimal, permuted, and other alternative alignments of protein structures","display_name":"OPAAS: a web server for optimal, permuted, and other alternative alignments of protein structures","publication_year":2006,"publication_date":"2006-07-01","ids":{"openalex":"https://openalex.org/W2003353954","doi":"https://doi.org/10.1093/nar/gkl264","mag":"2003353954","pmid":"https://pubmed.ncbi.nlm.nih.gov/16845117"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkl264","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkl264","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_2/W95/7623481/gkl264.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/34/suppl_2/W95/7623481/gkl264.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5038346855","display_name":"Edward S.C. Shih","orcid":"https://orcid.org/0000-0002-8175-0393"},"institutions":[{"id":"https://openalex.org/I4210096666","display_name":"Institute of Biomedical Sciences, Academia Sinica","ror":"https://ror.org/00tk6s776","country_code":"TW","type":"facility","lineage":["https://openalex.org/I4210096666","https://openalex.org/I84653119"]}],"countries":["TW"],"is_corresponding":true,"raw_author_name":"E. S. C. Shih","raw_affiliation_strings":["Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan","Institute of Biomedical Sciences , Academia Sinica , Taipei 11529 , Taiwan "],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan","institution_ids":["https://openalex.org/I4210096666"]},{"raw_affiliation_string":"Institute of Biomedical Sciences , Academia Sinica , Taipei 11529 , Taiwan ","institution_ids":["https://openalex.org/I4210096666"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109139960","display_name":"Ruei-Chi Gan","orcid":null},"institutions":[{"id":"https://openalex.org/I4210096666","display_name":"Institute of Biomedical Sciences, Academia Sinica","ror":"https://ror.org/00tk6s776","country_code":"TW","type":"facility","lineage":["https://openalex.org/I4210096666","https://openalex.org/I84653119"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"R.-c. R. Gan","raw_affiliation_strings":["Institute of Biomedical Sciences, Academia Sinica Taipei 11529, Taiwan","Institute of Biomedical Sciences , Academia Sinica , Taipei 11529 , Taiwan "],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biomedical Sciences, Academia Sinica Taipei 11529, Taiwan","institution_ids":["https://openalex.org/I4210096666"]},{"raw_affiliation_string":"Institute of Biomedical Sciences , Academia Sinica , Taipei 11529 , Taiwan ","institution_ids":["https://openalex.org/I4210096666"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5039723620","display_name":"Ming\u2010Jing Hwang","orcid":"https://orcid.org/0000-0002-9657-5663"},"institutions":[{"id":"https://openalex.org/I4210096666","display_name":"Institute of Biomedical Sciences, Academia Sinica","ror":"https://ror.org/00tk6s776","country_code":"TW","type":"facility","lineage":["https://openalex.org/I4210096666","https://openalex.org/I84653119"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"M.-J. Hwang","raw_affiliation_strings":["Institute of Biomedical Sciences, Academia Sinica Taipei 11529, Taiwan","Institute of Biomedical Sciences , Academia Sinica , Taipei 11529 , Taiwan "],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biomedical Sciences, Academia Sinica Taipei 11529, Taiwan","institution_ids":["https://openalex.org/I4210096666"]},{"raw_affiliation_string":"Institute of Biomedical Sciences , Academia Sinica , Taipei 11529 , Taiwan ","institution_ids":["https://openalex.org/I4210096666"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5038346855"],"corresponding_institution_ids":["https://openalex.org/I4210096666"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":0.8182,"has_fulltext":true,"cited_by_count":22,"citation_normalized_percentile":{"value":0.6983164,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"34","issue":"Web Server","first_page":"W95","last_page":"W98"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9980999827384949,"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":0.9980999827384949,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9972000122070312,"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"}},{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9890000224113464,"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/biology","display_name":"Biology","score":0.9570640325546265},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.6258658170700073},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5120273232460022},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4156697690486908},{"id":"https://openalex.org/keywords/web-site","display_name":"Web site","score":0.41499772667884827},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3834131360054016},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.28137439489364624},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.1574675440788269},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.1331770122051239}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.9570640325546265},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.6258658170700073},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5120273232460022},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4156697690486908},{"id":"https://openalex.org/C2984519610","wikidata":"https://www.wikidata.org/wiki/Q35127","display_name":"Web site","level":3,"score":0.41499772667884827},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3834131360054016},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.28137439489364624},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.1574675440788269},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.1331770122051239}],"mesh":[{"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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":7,"locations":[{"id":"doi:10.1093/nar/gkl264","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkl264","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_2/W95/7623481/gkl264.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:16845117","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16845117","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.104.666","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.104.666","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/cgi/reprint/34/suppl_2/W95.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.276.3202","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.276.3202","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/91/c9/Nucleic_Acids_Res_2006_Jul_1_34(Web_Server_issue)_W95-W98.tar.gz","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.594.2492","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.594.2492","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/content/34/suppl_2/W95.full-text-lowres.pdf","raw_type":"text"},{"id":"pmh:oai:europepmc.org:338428","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC1538888","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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:1538888","is_oa":true,"landing_page_url":"http://doi.org/10.1093/nar/gkl264","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":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkl264","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkl264","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_2/W95/7623481/gkl264.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321040","display_name":"National Science Council","ror":"https://ror.org/02kv4zf79"},{"id":"https://openalex.org/F4320321041","display_name":"Academia Sinica","ror":"https://ror.org/05bxb3784"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2003353954.pdf","grobid_xml":"https://content.openalex.org/works/W2003353954.grobid-xml"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W1965910641","https://openalex.org/W1967623938","https://openalex.org/W1975453400","https://openalex.org/W1983747555","https://openalex.org/W2011952909","https://openalex.org/W2022395419","https://openalex.org/W2023790301","https://openalex.org/W2027853992","https://openalex.org/W2053281575","https://openalex.org/W2053366984","https://openalex.org/W2056807348","https://openalex.org/W2073338969","https://openalex.org/W2077122857","https://openalex.org/W2077529366","https://openalex.org/W2077813307","https://openalex.org/W2085277871","https://openalex.org/W2087151779","https://openalex.org/W2089085945","https://openalex.org/W2116435022","https://openalex.org/W2118851904","https://openalex.org/W2121293808","https://openalex.org/W2130479394","https://openalex.org/W2148376194","https://openalex.org/W2151192631","https://openalex.org/W2152183846","https://openalex.org/W2152326664","https://openalex.org/W2163016858","https://openalex.org/W4239426826","https://openalex.org/W4254459749"],"related_works":["https://openalex.org/W4252337189","https://openalex.org/W3002947890","https://openalex.org/W2503502284","https://openalex.org/W2150024885","https://openalex.org/W2124166611","https://openalex.org/W2731820460","https://openalex.org/W1982472807","https://openalex.org/W2472303777","https://openalex.org/W100434825","https://openalex.org/W2475508055"],"abstract_inverted_index":{"The":[0],"large":[1],"number":[2],"of":[3,53,82,95,100,115,123],"experimentally":[4],"determined":[5],"protein":[6,15,20,34],"3D":[7],"structures":[8],"is":[9,24,66,162],"a":[10,25,43,73,135],"rich":[11],"resource":[12],"for":[13,28],"studying":[14],"function":[16],"and":[17,19,45,143],"evolution,":[18],"structure":[21],"comparison":[22],"(PSC)":[23],"key":[26],"method":[27,76,103],"such":[29],"studies.":[30],"When":[31],"comparing":[32],"two":[33,147],"structures,":[35],"almost":[36],"all":[37,93,122],"currently":[38],"available":[39],"PSC":[40,75,102,168],"servers":[41],"report":[42],"single":[44],"sequential":[46],"(i.e.":[47,61],"topological)":[48],"alignment,":[49],"whereas":[50],"the":[51,98,124,140],"existence":[52],"good":[54],"alternative":[55,80,126,131],"alignments,":[56],"including":[57,89],"those":[58],"involving":[59],"permutations":[60,91],"non-sequential":[62],"or":[63],"non-topological":[64],"alignments),":[65],"well":[67],"known.":[68],"We":[69],"have":[70],"recently":[71],"developed":[72],"novel":[74],"that":[77,161],"can":[78,133,150],"detect":[79],"alignments":[81,127,132],"statistical":[83],"significance":[84],"(alignment":[85],"similarity":[86],"P-value":[87],"<10(-5)),":[88],"structural":[90,154],"at":[92,106],"levels":[94],"complexity.":[96],"OPAAS,":[97],"server":[99],"this":[101],"freely":[104],"accessible":[105],"our":[107],"website":[108],"(http://opaas.ibms.sinica.edu.tw),":[109],"provides":[110],"an":[111],"easy-to-read":[112],"hierarchical":[113],"layout":[114],"output":[116],"to":[117,157],"display":[118],"detailed":[119],"information":[120],"on":[121,139],"significant":[125],"detected.":[128],"Because":[129],"these":[130],"offer":[134],"more":[136],"complete":[137],"picture":[138],"structural,":[141],"evolutionary":[142],"functional":[144],"relationship":[145],"between":[146],"proteins,":[148],"OPAAS":[149],"be":[151],"used":[152],"in":[153],"bioinformatics":[155],"research":[156],"gain":[158],"additional":[159],"insight":[160],"not":[163],"readily":[164],"provided":[165],"by":[166],"existing":[167],"servers.":[169]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-06-25T06:16:34.145877","created_date":"2025-10-10T00:00:00"}
