{"id":"https://openalex.org/W1981852402","doi":"https://doi.org/10.1109/bibe.2008.4696701","title":"Distance-based indexing of residue contacts for protein structure retrieval and alignment","display_name":"Distance-based indexing of residue contacts for protein structure retrieval and alignment","publication_year":2008,"publication_date":"2008-10-01","ids":{"openalex":"https://openalex.org/W1981852402","doi":"https://doi.org/10.1109/bibe.2008.4696701","mag":"1981852402"},"language":"en","primary_location":{"id":"doi:10.1109/bibe.2008.4696701","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2008.4696701","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2008 8th IEEE International Conference on BioInformatics and BioEngineering","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://hdl.handle.net/11511/41432","any_repository_has_fulltext":true},"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":false,"raw_author_name":"Ahmet Sacan","raw_affiliation_strings":["Computer Engineering Department, Middle East Technical University, Ankara, Turkey","Department of Computer Science & Engineering, Ohio State Uinversity, Columbus, OH, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Engineering Department, Middle East Technical University, Ankara, Turkey","institution_ids":["https://openalex.org/I201799495"]},{"raw_affiliation_string":"Department of Computer Science & Engineering, Ohio State Uinversity, Columbus, OH, USA","institution_ids":["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"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"I. Hakki Toroslu","raw_affiliation_strings":["Computer Engineering Department, Middle East Technical University, Ankara, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Engineering Department, Middle East Technical University, Ankara, Turkey","institution_ids":["https://openalex.org/I201799495"]}]},{"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/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hakan Ferhatosmanoglu","raw_affiliation_strings":["Department of Computer Science & Engineering, Ohio State Uinversity, Columbus, OH, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science & Engineering, Ohio State Uinversity, Columbus, OH, USA","institution_ids":["https://openalex.org/I52357470"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.09454177,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"1","issue":null,"first_page":"1","last_page":"7"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9969000220298767,"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":0.9969000220298767,"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":0.9933000206947327,"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":0.9836000204086304,"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/search-engine-indexing","display_name":"Search engine indexing","score":0.7663156986236572},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6972444653511047},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.660822868347168},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.5377187132835388},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5140632390975952},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"Structural alignment","score":0.5128607749938965},{"id":"https://openalex.org/keywords/protein-function","display_name":"Protein function","score":0.5075794458389282},{"id":"https://openalex.org/keywords/residue","display_name":"Residue (chemistry)","score":0.42166486382484436},{"id":"https://openalex.org/keywords/protein-structure-database","display_name":"Protein structure database","score":0.41756972670555115},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3909044861793518},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2559521794319153},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.24859583377838135},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11905500292778015},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.0815083384513855}],"concepts":[{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.7663156986236572},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6972444653511047},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.660822868347168},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.5377187132835388},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5140632390975952},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.5128607749938965},{"id":"https://openalex.org/C2986374874","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Protein function","level":3,"score":0.5075794458389282},{"id":"https://openalex.org/C2781338088","wikidata":"https://www.wikidata.org/wiki/Q903495","display_name":"Residue (chemistry)","level":2,"score":0.42166486382484436},{"id":"https://openalex.org/C136475424","wikidata":"https://www.wikidata.org/wiki/Q7251500","display_name":"Protein structure database","level":4,"score":0.41756972670555115},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3909044861793518},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2559521794319153},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.24859583377838135},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11905500292778015},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.0815083384513855},{"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/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/bibe.2008.4696701","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2008.4696701","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2008 8th IEEE International Conference on BioInformatics and BioEngineering","raw_type":"proceedings-article"},{"id":"pmh:oai:open.metu.edu.tr:11511/41432","is_oa":true,"landing_page_url":"https://hdl.handle.net/11511/41432","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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Conference Paper"}],"best_oa_location":{"id":"pmh:oai:open.metu.edu.tr:11511/41432","is_oa":true,"landing_page_url":"https://hdl.handle.net/11511/41432","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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Conference Paper"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":43,"referenced_works":["https://openalex.org/W42096393","https://openalex.org/W1523134890","https://openalex.org/W1930315378","https://openalex.org/W1977618577","https://openalex.org/W1979147581","https://openalex.org/W1992208183","https://openalex.org/W2004026586","https://openalex.org/W2008708467","https://openalex.org/W2009836662","https://openalex.org/W2016685072","https://openalex.org/W2018934172","https://openalex.org/W2022058405","https://openalex.org/W2024991751","https://openalex.org/W2042786254","https://openalex.org/W2049437675","https://openalex.org/W2055043387","https://openalex.org/W2062351773","https://openalex.org/W2074231493","https://openalex.org/W2085277871","https://openalex.org/W2099698841","https://openalex.org/W2100126267","https://openalex.org/W2103612114","https://openalex.org/W2108107014","https://openalex.org/W2113563422","https://openalex.org/W2123956446","https://openalex.org/W2126016150","https://openalex.org/W2130479394","https://openalex.org/W2133657429","https://openalex.org/W2133715954","https://openalex.org/W2142375194","https://openalex.org/W2148823738","https://openalex.org/W2151430326","https://openalex.org/W2152024417","https://openalex.org/W2152326664","https://openalex.org/W2158714788","https://openalex.org/W2160299673","https://openalex.org/W2161151688","https://openalex.org/W4236236547","https://openalex.org/W4248987599","https://openalex.org/W6601702993","https://openalex.org/W6631163696","https://openalex.org/W6648393565","https://openalex.org/W6652751874"],"related_works":["https://openalex.org/W3042805293","https://openalex.org/W4389053053","https://openalex.org/W2903170547","https://openalex.org/W2040770994","https://openalex.org/W4383473004","https://openalex.org/W2969133412","https://openalex.org/W2155238244","https://openalex.org/W2099254366","https://openalex.org/W1989756167","https://openalex.org/W2470147982"],"abstract_inverted_index":{"New":[0],"protein":[1,22,101,125,213],"structures":[2],"are":[3,25,33,58,155,188,219],"continuously":[4],"being":[5],"determined":[6],"with":[7],"the":[8,14,38,47,86,202,209,212],"hope":[9],"of":[10,18,46,77,89,116,123,137,148,204],"deriving":[11],"insights":[12],"into":[13,157],"function":[15,132],"and":[16,20,29,43,113,216],"mechanisms":[17],"proteins,":[19,178],"consequently,":[21],"structure":[23,102,214],"repositories":[24],"growing":[26],"by":[27,196],"leaps":[28],"bounds.":[30],"However,":[31],"we":[32,97],"still":[34],"far":[35],"from":[36,120],"having":[37],"right":[39],"methods":[40],"for":[41,60,133,145],"sensitive":[42],"effective":[44,172],"use":[45],"available":[48,124],"structural":[49,55,92,164,185],"data.":[50],"The":[51,166],"fact":[52],"that":[53,69,108,169,187],"current":[54],"analysis":[56],"tools":[57],"impractical":[59],"large-scale":[61],"applications":[62],"have":[63],"given":[64],"rise":[65],"to":[66,71,190],"several":[67],"approaches":[68,82],"try":[70],"quickly":[72],"identify":[73],"candidate":[74],"proteins":[75],"worthy":[76],"further":[78],"analysis.":[79],"Nonetheless,":[80],"these":[81],"do":[83],"not":[84,174],"provide":[85],"desired":[87],"sensitivity":[88],"identifying":[90,176],"important":[91],"similarities.":[93],"In":[94],"this":[95,207],"study,":[96],"propose":[98],"a":[99,121,129],"new":[100],"retrieval":[103,147,215],"method":[104],"(RCIndex:":[105],"Residue-Contacts":[106],"Index)":[107],"is":[109,142,171,208],"based":[110],"on":[111],"accurate":[112],"efficient":[114],"identification":[115],"similar":[117,149],"residue":[118,138,150],"contacts":[119],"database":[122],"structures.":[126],"By":[127],"defining":[128],"metric":[130],"distance":[131],"biologically":[134],"meaningful":[135],"comparison":[136],"contacts,":[139],"distance-based":[140],"indexing":[141],"made":[143],"applicable":[144],"quick":[146],"contact":[151],"seeds.":[152],"These":[153],"seeds":[154],"extended":[156],"high":[158,183],"scoring":[159],"segment":[160],"pairs,":[161],"which":[162],"induce":[163],"superpositions.":[165],"results":[167],"show":[168],"RCIndex":[170],"in":[173],"only":[175],"related":[177],"but":[179],"also":[180],"producing":[181],"remarkably":[182],"quality":[184],"alignments":[186],"comparable":[189],"or":[191],"better":[192],"than":[193],"those":[194],"produced":[195],"popular":[197],"pairwise":[198],"alignment":[199,217],"tools.":[200],"To":[201],"best":[203],"our":[205],"knowledge,":[206],"first":[210],"time":[211],"tasks":[218],"successfully":[220],"handled":[221],"together.":[222]},"counts_by_year":[{"year":2012,"cited_by_count":1}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}
