{"id":"https://openalex.org/W2114854952","doi":"https://doi.org/10.1093/nar/gku394","title":"POSA: a user-driven, interactive multiple protein structure alignment server","display_name":"POSA: a user-driven, interactive multiple protein structure alignment server","publication_year":2014,"publication_date":"2014-05-16","ids":{"openalex":"https://openalex.org/W2114854952","doi":"https://doi.org/10.1093/nar/gku394","mag":"2114854952","pmid":"https://pubmed.ncbi.nlm.nih.gov/24838569"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gku394","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gku394","pdf_url":"https://academic.oup.com/nar/article-pdf/42/W1/W240/17423163/gku394.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/42/W1/W240/17423163/gku394.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5072166385","display_name":"Zhanwen Li","orcid":null},"institutions":[{"id":"https://openalex.org/I188891513","display_name":"Sanford Burnham Prebys Medical Discovery Institute","ror":"https://ror.org/03m1g2s55","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I188891513"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Zhanwen Li","raw_affiliation_strings":["Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA"],"affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA","institution_ids":["https://openalex.org/I188891513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108489138","display_name":"P. Natarajan","orcid":null},"institutions":[{"id":"https://openalex.org/I188891513","display_name":"Sanford Burnham Prebys Medical Discovery Institute","ror":"https://ror.org/03m1g2s55","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I188891513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Padmaja Natarajan","raw_affiliation_strings":["Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA"],"affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA","institution_ids":["https://openalex.org/I188891513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082620694","display_name":"Yuzhen Ye","orcid":"https://orcid.org/0000-0003-3707-3185"},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuzhen Ye","raw_affiliation_strings":["School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA","School of Informatics and Computing, Indiana University - Bloomington, IN 47405, USA"],"affiliations":[{"raw_affiliation_string":"School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA","institution_ids":["https://openalex.org/I4210119109"]},{"raw_affiliation_string":"School of Informatics and Computing, Indiana University - Bloomington, IN 47405, USA","institution_ids":["https://openalex.org/I4210119109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048396734","display_name":"Thomas Hrabe","orcid":null},"institutions":[{"id":"https://openalex.org/I188891513","display_name":"Sanford Burnham Prebys Medical Discovery Institute","ror":"https://ror.org/03m1g2s55","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I188891513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thomas Hrabe","raw_affiliation_strings":["Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA"],"affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA","institution_ids":["https://openalex.org/I188891513"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010671148","display_name":"Adam Godzik","orcid":"https://orcid.org/0000-0002-2425-852X"},"institutions":[{"id":"https://openalex.org/I188891513","display_name":"Sanford Burnham Prebys Medical Discovery Institute","ror":"https://ror.org/03m1g2s55","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I188891513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Adam Godzik","raw_affiliation_strings":["Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA adam@godziklab.org","Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA"],"affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA adam@godziklab.org","institution_ids":[]},{"raw_affiliation_string":"Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA","institution_ids":["https://openalex.org/I188891513"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5072166385"],"corresponding_institution_ids":["https://openalex.org/I188891513"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":1.426,"has_fulltext":true,"cited_by_count":62,"citation_normalized_percentile":{"value":0.81393489,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"42","issue":"W1","first_page":"W240","last_page":"W245"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9965999722480774,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9965999722480774,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9965999722480774,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9945999979972839,"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/login","display_name":"Login","score":0.6746475696563721},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6513304114341736},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.6053764820098877},{"id":"https://openalex.org/keywords/user-interface","display_name":"User interface","score":0.5032173991203308},{"id":"https://openalex.org/keywords/password","display_name":"Password","score":0.4130502939224243},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3945196270942688},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.20477747917175293},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.18369612097740173}],"concepts":[{"id":"https://openalex.org/C113324615","wikidata":"https://www.wikidata.org/wiki/Q472302","display_name":"Login","level":2,"score":0.6746475696563721},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6513304114341736},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6053764820098877},{"id":"https://openalex.org/C89505385","wikidata":"https://www.wikidata.org/wiki/Q47146","display_name":"User interface","level":2,"score":0.5032173991203308},{"id":"https://openalex.org/C109297577","wikidata":"https://www.wikidata.org/wiki/Q161157","display_name":"Password","level":2,"score":0.4130502939224243},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3945196270942688},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.20477747917175293},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.18369612097740173}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"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":"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":6,"locations":[{"id":"doi:10.1093/nar/gku394","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gku394","pdf_url":"https://academic.oup.com/nar/article-pdf/42/W1/W240/17423163/gku394.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:24838569","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24838569","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:ark:/13030/qt298851fn","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.802.5021","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.802.5021","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/67/32/gku394.PMC4086100.pdf","raw_type":"text"},{"id":"pmh:oai:escholarship.org/ark:/13030/qt298851fn","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/298851fn","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic acids research, vol 42, iss Web Server issue","raw_type":"article"},{"id":"pmh:oai:europepmc.org:3176839","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4086100","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"}],"best_oa_location":{"id":"doi:10.1093/nar/gku394","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gku394","pdf_url":"https://academic.oup.com/nar/article-pdf/42/W1/W240/17423163/gku394.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":[{"id":"https://openalex.org/G3611247453","display_name":null,"funder_award_id":"R01GM","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3817829172","display_name":null,"funder_award_id":"GM101457","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2114854952.pdf","grobid_xml":"https://content.openalex.org/works/W2114854952.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W1534782460","https://openalex.org/W1535715635","https://openalex.org/W1905708630","https://openalex.org/W1967538863","https://openalex.org/W1969153299","https://openalex.org/W2006754101","https://openalex.org/W2019877779","https://openalex.org/W2031901496","https://openalex.org/W2048620321","https://openalex.org/W2058149030","https://openalex.org/W2077529366","https://openalex.org/W2084482738","https://openalex.org/W2090617952","https://openalex.org/W2097642323","https://openalex.org/W2126996906","https://openalex.org/W2132629607","https://openalex.org/W2135303325","https://openalex.org/W2159774316","https://openalex.org/W2168926448","https://openalex.org/W2168964504","https://openalex.org/W6632175362","https://openalex.org/W6639816060"],"related_works":["https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W4256170434","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W4233948907","https://openalex.org/W2013243191"],"abstract_inverted_index":{"POSA":[0,65],"(Partial":[1],"Order":[2],"Structure":[3],"Alignment),":[4],"available":[5],"at":[6],"http://posa.godziklab.org,":[7],"is":[8,35,44,50,75,126],"a":[9,119,159],"server":[10,66],"for":[11,147],"multiple":[12,151],"protein":[13],"structure":[14,25,152],"alignment":[15,26,91,114],"introduced":[16],"in":[17,58,92,141,158,174,188],"2005":[18],"(Ye,Y.":[19],"and":[20,37,42,55,108,115,179],"Godzik,A.":[21],"(2005)":[22],"Multiple":[23],"flexible":[24],"using":[27],"partial":[28],"order":[29],"graphs.":[30],"Bioinformatics,":[31],"21,":[32],"2362-2369).":[33],"It":[34],"free":[36],"open":[38],"to":[39,53,81,102,111,136],"all":[40,138],"users,":[41],"there":[43,49],"no":[45],"login":[46],"requirement,":[47],"albeit":[48],"an":[51,76,127],"option":[52],"register":[54],"store":[56],"results":[57,149],"individual,":[59],"password-protected":[60],"directories.":[61],"In":[62],"the":[63,79,90,113,134,177],"updated":[64],"described":[67],"here,":[68],"we":[69],"introduce":[70],"two":[71],"significant":[72],"improvements.":[73],"First":[74],"interface":[77,99],"allowing":[78],"user":[80,135,170],"provide":[82],"additional":[83],"information":[84],"by":[85],"defining":[86],"segments":[87],"that":[88,132],"anchor":[89],"one":[93,142],"or":[94,154,182],"more":[95],"input":[96],"structures.":[97],"This":[98],"allows":[100],"users":[101],"take":[103],"advantage":[104],"of":[105,150,161,176],"their":[106],"intuition":[107],"biological":[109],"insights":[110],"improve":[112],"guide":[116],"it":[117],"toward":[118],"biologically":[120],"relevant":[121],"solution.":[122],"The":[123,169],"second":[124],"improvement":[125],"interactive":[128],"visualization":[129,167],"with":[130,164],"options":[131],"allow":[133],"view":[137,155],"superposed":[139],"structures":[140,185],"window":[143],"(a":[144],"typical":[145],"solution":[146],"visualizing":[148],"alignments)":[153],"them":[156],"individually":[157],"series":[160],"synchronized":[162],"windows":[163,178],"extensive,":[165],"user-controlled":[166],"options.":[168],"can":[171],"rotate":[172],"structure(s)":[173],"any":[175],"study":[180],"similarities":[181],"differences":[183],"between":[184],"clearly":[186],"visible":[187],"individual":[189],"windows.":[190]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":10},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
