{"id":"https://openalex.org/W2110821243","doi":"https://doi.org/10.1109/tai.2003.1250163","title":"Pairwise protein structure alignment based on an orientation-independent representation of the backbone geometry","display_name":"Pairwise protein structure alignment based on an orientation-independent representation of the backbone geometry","publication_year":2004,"publication_date":"2004-03-02","ids":{"openalex":"https://openalex.org/W2110821243","doi":"https://doi.org/10.1109/tai.2003.1250163","mag":"2110821243"},"language":"en","primary_location":{"id":"doi:10.1109/tai.2003.1250163","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tai.2003.1250163","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings. 15th IEEE International Conference on Tools with Artificial Intelligence","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://hdl.handle.net/11299/215544","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010419481","display_name":"Jieping Ye","orcid":"https://orcid.org/0000-0001-8662-5818"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jieping Ye","raw_affiliation_strings":["Department of Computer Science & Engineering, University of Minnesota, Minneapolis, MN, USA","Department of Computer Science and Engineering University of Minnesota , Minneapolis , MN , USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science & Engineering, University of Minnesota, Minneapolis, MN, USA","institution_ids":["https://openalex.org/I130238516"]},{"raw_affiliation_string":"Department of Computer Science and Engineering University of Minnesota , Minneapolis , MN , USA","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050894676","display_name":"Ravi Janardan","orcid":"https://orcid.org/0000-0003-3922-6763"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"R. Janardan","raw_affiliation_strings":["Department of Computer Science & Engineering, University of Minnesota, Minneapolis, MN, USA","Department of Computer Science and Engineering University of Minnesota , Minneapolis , MN , USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science & Engineering, University of Minnesota, Minneapolis, MN, USA","institution_ids":["https://openalex.org/I130238516"]},{"raw_affiliation_string":"Department of Computer Science and Engineering University of Minnesota , Minneapolis , MN , USA","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062314906","display_name":"Song\u2010Tao Liu","orcid":"https://orcid.org/0000-0002-9623-8579"},"institutions":[{"id":"https://openalex.org/I154425047","display_name":"University of Alberta","ror":"https://ror.org/0160cpw27","country_code":"CA","type":"education","lineage":["https://openalex.org/I154425047"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Songtao Liu","raw_affiliation_strings":["Department of Mathematics, University of Alberta, Edmonton, AB, Canada","University of Alberta"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics, University of Alberta, Edmonton, AB, Canada","institution_ids":["https://openalex.org/I154425047"]},{"raw_affiliation_string":"University of Alberta","institution_ids":["https://openalex.org/I154425047"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5010419481"],"corresponding_institution_ids":["https://openalex.org/I130238516"],"apc_list":null,"apc_paid":null,"fwci":0.3618,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.5914931,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"273","issue":null,"first_page":"2","last_page":"9"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9991999864578247,"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":0.9991999864578247,"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":0.9948999881744385,"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":0.9947999715805054,"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/representation","display_name":"Representation (politics)","score":0.6908196210861206},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.661554217338562},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5667380094528198},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"Structural alignment","score":0.5621368288993835},{"id":"https://openalex.org/keywords/orientation","display_name":"Orientation (vector space)","score":0.5118135809898376},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4909825623035431},{"id":"https://openalex.org/keywords/space","display_name":"Space (punctuation)","score":0.41467708349227905},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.4079245328903198},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3055380582809448},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.2596539855003357},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.18509525060653687}],"concepts":[{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.6908196210861206},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.661554217338562},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5667380094528198},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.5621368288993835},{"id":"https://openalex.org/C16345878","wikidata":"https://www.wikidata.org/wiki/Q107472979","display_name":"Orientation (vector space)","level":2,"score":0.5118135809898376},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4909825623035431},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.41467708349227905},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.4079245328903198},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3055380582809448},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.2596539855003357},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.18509525060653687},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"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/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/tai.2003.1250163","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tai.2003.1250163","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings. 15th IEEE International Conference on Tools with Artificial Intelligence","raw_type":"proceedings-article"},{"id":"pmh:oai:conservancy.umn.edu:11299/215544","is_oa":true,"landing_page_url":"http://hdl.handle.net/11299/215544","pdf_url":"http://hdl.handle.net/11299/215544","source":{"id":"https://openalex.org/S4306402521","display_name":"University of Minnesota Digital Conservancy (University of Minnesota)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I130238516","host_organization_name":"University of Minnesota","host_organization_lineage":["https://openalex.org/I130238516"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Report"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.1.8893","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1.8893","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www-users.cs.umn.edu/~jieping/Pairwise_ictai03.ps","raw_type":"text"}],"best_oa_location":{"id":"pmh:oai:conservancy.umn.edu:11299/215544","is_oa":true,"landing_page_url":"http://hdl.handle.net/11299/215544","pdf_url":"http://hdl.handle.net/11299/215544","source":{"id":"https://openalex.org/S4306402521","display_name":"University of Minnesota Digital Conservancy (University of Minnesota)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I130238516","host_organization_name":"University of Minnesota","host_organization_lineage":["https://openalex.org/I130238516"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Report"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2110821243.pdf"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W938539187","https://openalex.org/W1491063910","https://openalex.org/W1520321564","https://openalex.org/W1573510965","https://openalex.org/W1627086342","https://openalex.org/W1966521833","https://openalex.org/W1979147581","https://openalex.org/W2004935122","https://openalex.org/W2011039300","https://openalex.org/W2012744602","https://openalex.org/W2021953523","https://openalex.org/W2022058405","https://openalex.org/W2023790301","https://openalex.org/W2085277871","https://openalex.org/W2094533318","https://openalex.org/W2097471670","https://openalex.org/W2110821243","https://openalex.org/W2130479394","https://openalex.org/W2152326664","https://openalex.org/W2170210017","https://openalex.org/W2610179052","https://openalex.org/W2611102240","https://openalex.org/W2798909945","https://openalex.org/W2907227701","https://openalex.org/W4285719527","https://openalex.org/W6676426289"],"related_works":["https://openalex.org/W2487162673","https://openalex.org/W2793211469","https://openalex.org/W2949152769","https://openalex.org/W4372354731","https://openalex.org/W2942366970","https://openalex.org/W2807634898","https://openalex.org/W1692008701","https://openalex.org/W3042805293","https://openalex.org/W4389053053","https://openalex.org/W2903170547"],"abstract_inverted_index":{"Determining":[0],"structural":[1],"similarities":[2],"between":[3],"proteins":[4],"is":[5,23,61,82,91],"an":[6,21,78],"important":[7],"problem":[8],"since":[9],"it":[10],"can":[11],"help":[12],"identify":[13],"functional":[14],"and":[15,69,102,106,111],"evolutionary":[16],"relationships.":[17],"In":[18],"this":[19,74],"paper,":[20],"algorithm":[22,35,53,90],"proposed":[24],"to":[25,73,76],"align":[26],"two":[27,94],"protein":[28,32],"structures.":[29],"Given":[30],"the":[31,34,44,58,89],"backbones,":[33],"finds":[36],"a":[37,55],"rigid":[38],"motion":[39],"of":[40,57,63],"one":[41],"backbone":[42],"onto":[43],"other":[45],"such":[46],"that":[47,60,88],"large":[48],"substructures":[49],"are":[50],"matched.":[51],"The":[52],"uses":[54],"representation":[56,75],"backbones":[59],"independent":[62],"their":[64],"relative":[65],"orientations":[66],"in":[67],"space":[68],"applies":[70],"dynamic":[71],"programming":[72],"compute":[77],"initial":[79],"alignment,":[80],"which":[81],"then":[83],"refined":[84],"iteratively.":[85],"Experiments":[86],"indicate":[87],"competitive":[92],"with":[93],"well-known":[95],"algorithms,":[96],"namely":[97],"DALI":[98],"by":[99,108],"L.":[100],"Holm":[101],"C.":[103],"Sander":[104],"(1993)":[105],"LOCK":[107],"A.P.":[109],"Singh":[110],"D.L.":[112],"Brutlag":[113],"(1997).":[114]},"counts_by_year":[],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
