{"id":"https://openalex.org/W2118249785","doi":"https://doi.org/10.1093/bioinformatics/btn545","title":"Integrated search and alignment of protein structures","display_name":"Integrated search and alignment of protein structures","publication_year":2008,"publication_date":"2008-10-22","ids":{"openalex":"https://openalex.org/W2118249785","doi":"https://doi.org/10.1093/bioinformatics/btn545","mag":"2118249785","pmid":"https://pubmed.ncbi.nlm.nih.gov/18945684"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btn545","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn545","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5016398897","display_name":"Ahmet Sa\u00e7an","orcid":"https://orcid.org/0000-0002-3570-3270"},"institutions":[{"id":"https://openalex.org/I201799495","display_name":"Middle East Technical University","ror":"https://ror.org/014weej12","country_code":"TR","type":"education","lineage":["https://openalex.org/I201799495"]},{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["TR","US"],"is_corresponding":true,"raw_author_name":"Ahmet Sacan","raw_affiliation_strings":["1 Department of Computer Engineering, Middle East Technical University, Ankara, Turkey, 2Department of Computer, Science and Engineering and 3Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Computer Engineering, Middle East Technical University, Ankara, Turkey, 2Department of Computer, Science and Engineering and 3Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA","institution_ids":["https://openalex.org/I201799495","https://openalex.org/I52357470"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039253696","display_name":"\u0130smail Hakk\u0131 Toroslu","orcid":"https://orcid.org/0000-0002-4524-8232"},"institutions":[{"id":"https://openalex.org/I201799495","display_name":"Middle East Technical University","ror":"https://ror.org/014weej12","country_code":"TR","type":"education","lineage":["https://openalex.org/I201799495"]},{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["TR","US"],"is_corresponding":false,"raw_author_name":"I. Hakki Toroslu","raw_affiliation_strings":["1 Department of Computer Engineering, Middle East Technical University, Ankara, Turkey, 2Department of Computer, Science and Engineering and 3Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Computer Engineering, Middle East Technical University, Ankara, Turkey, 2Department of Computer, Science and Engineering and 3Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA","institution_ids":["https://openalex.org/I201799495","https://openalex.org/I52357470"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078571347","display_name":"Hakan Ferhatosmano\u011flu","orcid":"https://orcid.org/0000-0002-5181-4712"},"institutions":[{"id":"https://openalex.org/I201799495","display_name":"Middle East Technical University","ror":"https://ror.org/014weej12","country_code":"TR","type":"education","lineage":["https://openalex.org/I201799495"]},{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["TR","US"],"is_corresponding":false,"raw_author_name":"Hakan Ferhatosmanoglu","raw_affiliation_strings":["1 Department of Computer Engineering, Middle East Technical University, Ankara, Turkey, 2Department of Computer, Science and Engineering and 3Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Computer Engineering, Middle East Technical University, Ankara, Turkey, 2Department of Computer, Science and Engineering and 3Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA","institution_ids":["https://openalex.org/I201799495","https://openalex.org/I52357470"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5016398897"],"corresponding_institution_ids":["https://openalex.org/I201799495","https://openalex.org/I52357470"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":1.4603,"has_fulltext":false,"cited_by_count":22,"citation_normalized_percentile":{"value":0.81296683,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"24","issue":"24","first_page":"2872","last_page":"2879"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.8852999806404114,"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":0.8852999806404114,"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":0.08160000294446945,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.004000000189989805,"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/computer-science","display_name":"Computer science","score":0.7508691549301147},{"id":"https://openalex.org/keywords/search-engine-indexing","display_name":"Search engine indexing","score":0.7376578450202942},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"Structural alignment","score":0.593641459941864},{"id":"https://openalex.org/keywords/protein-structure-database","display_name":"Protein structure database","score":0.5221667289733887},{"id":"https://openalex.org/keywords/metric","display_name":"Metric (unit)","score":0.5106201767921448},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.5035480856895447},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5020298957824707},{"id":"https://openalex.org/keywords/nearest-neighbor-search","display_name":"Nearest neighbor search","score":0.45959314703941345},{"id":"https://openalex.org/keywords/voronoi-diagram","display_name":"Voronoi diagram","score":0.43668797612190247},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4243066906929016},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.42136043310165405},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.29100388288497925},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.10921633243560791},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08098509907722473}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7508691549301147},{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.7376578450202942},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.593641459941864},{"id":"https://openalex.org/C136475424","wikidata":"https://www.wikidata.org/wiki/Q7251500","display_name":"Protein structure database","level":4,"score":0.5221667289733887},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.5106201767921448},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.5035480856895447},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5020298957824707},{"id":"https://openalex.org/C116738811","wikidata":"https://www.wikidata.org/wiki/Q608751","display_name":"Nearest neighbor search","level":2,"score":0.45959314703941345},{"id":"https://openalex.org/C24881265","wikidata":"https://www.wikidata.org/wiki/Q757267","display_name":"Voronoi diagram","level":2,"score":0.43668797612190247},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4243066906929016},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.42136043310165405},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.29100388288497925},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.10921633243560791},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08098509907722473},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C41584329","wikidata":"https://www.wikidata.org/wiki/Q175902","display_name":"Sequence database","level":3,"score":0.0},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"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":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","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":true},{"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":"D017433","descriptor_name":"Protein Structure, Secondary","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":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","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":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","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":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btn545","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn545","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:18945684","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18945684","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":"Comparative Study"},{"id":"pmh:oai:https://open.metu.edu.tr:11511/37309","is_oa":false,"landing_page_url":"https://hdl.handle.net/11511/37309","pdf_url":null,"source":{"id":"https://openalex.org/S4306402495","display_name":"OpenMETU (Middle East Technical University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I201799495","host_organization_name":"Middle East Technical University","host_organization_lineage":["https://openalex.org/I201799495"],"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":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":53,"referenced_works":["https://openalex.org/W1523134890","https://openalex.org/W1930315378","https://openalex.org/W1968002069","https://openalex.org/W1974686816","https://openalex.org/W1977618577","https://openalex.org/W1978611087","https://openalex.org/W1992208183","https://openalex.org/W2004026586","https://openalex.org/W2008708467","https://openalex.org/W2009836662","https://openalex.org/W2022058405","https://openalex.org/W2023856819","https://openalex.org/W2024991751","https://openalex.org/W2026853762","https://openalex.org/W2042786254","https://openalex.org/W2049437675","https://openalex.org/W2062318714","https://openalex.org/W2062351773","https://openalex.org/W2062359859","https://openalex.org/W2073193878","https://openalex.org/W2074231493","https://openalex.org/W2085277871","https://openalex.org/W2099698841","https://openalex.org/W2100126267","https://openalex.org/W2100792189","https://openalex.org/W2103612114","https://openalex.org/W2107989651","https://openalex.org/W2108067237","https://openalex.org/W2108107014","https://openalex.org/W2113563422","https://openalex.org/W2121150070","https://openalex.org/W2123956446","https://openalex.org/W2125443524","https://openalex.org/W2126016150","https://openalex.org/W2129046747","https://openalex.org/W2133657429","https://openalex.org/W2133715954","https://openalex.org/W2135152200","https://openalex.org/W2137146016","https://openalex.org/W2141224484","https://openalex.org/W2142375194","https://openalex.org/W2145045494","https://openalex.org/W2148823738","https://openalex.org/W2152326664","https://openalex.org/W2153024955","https://openalex.org/W2157410466","https://openalex.org/W2158714788","https://openalex.org/W2161151688","https://openalex.org/W4316094799","https://openalex.org/W6631163696","https://openalex.org/W6644616578","https://openalex.org/W6648393565","https://openalex.org/W6652751874"],"related_works":["https://openalex.org/W1949910768","https://openalex.org/W1480566255","https://openalex.org/W2254397067","https://openalex.org/W2013685631","https://openalex.org/W1610355325","https://openalex.org/W1882921205","https://openalex.org/W2969133412","https://openalex.org/W2015399150","https://openalex.org/W1989756167","https://openalex.org/W2040770994"],"abstract_inverted_index":{"MOTIVATION:":[0],"Identification":[1],"and":[2,36,61,105,131,160],"comparison":[3],"of":[4,19,38,45,50,166],"similar":[5,124],"three-dimensional":[6],"(3D)":[7],"protein":[8,41,46,52,110,125],"structures":[9],"has":[10],"become":[11],"an":[12],"even":[13],"greater":[14],"challenge":[15],"in":[16,108,122,141],"the":[17,20,51,57,99,109,150,167],"face":[18],"rapidly":[21],"growing":[22],"structure":[23,59,111,129,138,169],"databases.":[24,112],"Here,":[25],"we":[26],"introduce":[27],"Vorometric,":[28],"a":[29,39,43,62,77,177],"new":[30],"method":[31,80],"that":[32,117],"provides":[33],"efficient":[34,70],"search":[35,104,142],"alignment":[37,106,170],"query":[40],"against":[42],"database":[44],"structures.":[47],"Voronoi":[48],"contacts":[49],"residues":[53],"are":[54,81,89,154],"enriched":[55],"with":[56,164],"secondary":[58],"information":[60],"metric":[63],"substitution":[64],"matrix":[65],"is":[66,98,119,174],"developed":[67],"to":[68,83,92,101,156],"allow":[69],"indexing.":[71],"The":[72,113],"contact":[73],"hits":[74],"obtained":[75],"from":[76],"distance-based":[78],"indexing":[79],"extended":[82],"obtain":[84],"high-scoring":[85],"segment":[86],"pairs,":[87],"which":[88],"then":[90],"used":[91],"generate":[93],"structural":[94,151],"alignments.":[95],"RESULTS:":[96],"Vorometric":[97,118,135,173],"first":[100],"address":[102],"both":[103],"problems":[107],"experimental":[114],"results":[115],"show":[116],"simultaneously":[120],"effective":[121],"retrieving":[123],"structures,":[126],"producing":[127],"high-quality":[128],"alignments,":[130],"identifying":[132],"cross-fold":[133],"similarities.":[134],"outperforms":[136],"current":[137],"retrieval":[139],"methods":[140],"accuracy,":[143],"while":[144],"requiring":[145],"com-parable":[146],"running":[147],"times.":[148],"Furthermore,":[149],"superpositions":[152],"produced":[153],"shown":[155],"have":[157],"better":[158],"quality":[159],"coverage,":[161],"when":[162],"compared":[163],"those":[165],"popular":[168],"tools.":[171],"AVAILABILITY:":[172],"available":[175],"as":[176],"web":[178],"service":[179],"at":[180],"http://bio.cse.ohio-state.edu/Vorometric":[181]},"counts_by_year":[{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":6}],"updated_date":"2026-08-27T14:10:00.468798","created_date":"2025-10-10T00:00:00"}
