{"id":"https://openalex.org/W4232453105","doi":"https://doi.org/10.1109/ipdps.2006.1639540","title":"A method to improve structural modeling based on conserved domain clusters","display_name":"A method to improve structural modeling based on conserved domain clusters","publication_year":2006,"publication_date":"2006-01-01","ids":{"openalex":"https://openalex.org/W4232453105","doi":"https://doi.org/10.1109/ipdps.2006.1639540"},"language":"en","primary_location":{"id":"doi:10.1109/ipdps.2006.1639540","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ipdps.2006.1639540","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings 20th IEEE International Parallel & Distributed Processing Symposium","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5100731978","display_name":"Fa Zhang","orcid":"https://orcid.org/0000-0002-2081-9369"},"institutions":[{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]},{"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":["CN","US"],"is_corresponding":true,"raw_author_name":"Fa Zhang","raw_affiliation_strings":["Department of Biomedical Information, Ohio State Uinversity, Columbus, OH, USA","Institute of Computing Technology, Chinese Academy and Sciences, Beijing, China"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Information, Ohio State Uinversity, Columbus, OH, USA","institution_ids":["https://openalex.org/I52357470"]},{"raw_affiliation_string":"Institute of Computing Technology, Chinese Academy and Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210090176"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029617420","display_name":"Lin Xu","orcid":"https://orcid.org/0000-0002-8967-919X"},"institutions":[{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lin Xu","raw_affiliation_strings":["Institute of Computing Technology, and Graduate Schools, Chinese Academy and Sciences, Beijing, China"],"affiliations":[{"raw_affiliation_string":"Institute of Computing Technology, and Graduate Schools, Chinese Academy and Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210090176"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100770277","display_name":"Bo Yuan","orcid":"https://orcid.org/0000-0002-0004-6733"},"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":"Bo Yuan","raw_affiliation_strings":["Department of Biomedical Information and Pharmacology, Ohio State Uinversity, Columbus, OH, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Information and Pharmacology, Ohio State Uinversity, Columbus, OH, USA","institution_ids":["https://openalex.org/I52357470"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5100731978"],"corresponding_institution_ids":["https://openalex.org/I4210090176","https://openalex.org/I52357470"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.33383229,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"5","issue":null,"first_page":"7 pp.","last_page":"7 pp."},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9986000061035156,"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":0.9986000061035156,"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":0.9936000108718872,"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/T10171","display_name":"Biofuel production and bioconversion","score":0.9904999732971191,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.769597053527832},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"Structural alignment","score":0.7688877582550049},{"id":"https://openalex.org/keywords/template","display_name":"Template","score":0.7334020137786865},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.704024612903595},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.6713036894798279},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.670093834400177},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.6116495132446289},{"id":"https://openalex.org/keywords/homology-modeling","display_name":"Homology modeling","score":0.6100558042526245},{"id":"https://openalex.org/keywords/protein-superfamily","display_name":"Protein superfamily","score":0.5607267618179321},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.532328724861145},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5252827405929565},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.5232766270637512},{"id":"https://openalex.org/keywords/structural-classification-of-proteins-database","display_name":"Structural Classification of Proteins database","score":0.4882564842700958},{"id":"https://openalex.org/keywords/protein-structure-database","display_name":"Protein structure database","score":0.48781922459602356},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4718988835811615},{"id":"https://openalex.org/keywords/protein-domain","display_name":"Protein domain","score":0.46431538462638855},{"id":"https://openalex.org/keywords/homology","display_name":"Homology (biology)","score":0.45870646834373474},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4501205086708069},{"id":"https://openalex.org/keywords/loop-modeling","display_name":"Loop modeling","score":0.42328715324401855},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.3065311312675476},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.2418023943901062},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1816832423210144},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1331779658794403},{"id":"https://openalex.org/keywords/sequence-database","display_name":"Sequence database","score":0.11077404022216797},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.10378941893577576},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.09966546297073364}],"concepts":[{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.769597053527832},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.7688877582550049},{"id":"https://openalex.org/C82714645","wikidata":"https://www.wikidata.org/wiki/Q438331","display_name":"Template","level":2,"score":0.7334020137786865},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.704024612903595},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.6713036894798279},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.670093834400177},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.6116495132446289},{"id":"https://openalex.org/C169627665","wikidata":"https://www.wikidata.org/wiki/Q5767913","display_name":"Homology modeling","level":3,"score":0.6100558042526245},{"id":"https://openalex.org/C178180057","wikidata":"https://www.wikidata.org/wiki/Q7251477","display_name":"Protein superfamily","level":3,"score":0.5607267618179321},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.532328724861145},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5252827405929565},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.5232766270637512},{"id":"https://openalex.org/C58773245","wikidata":"https://www.wikidata.org/wiki/Q4832556","display_name":"Structural Classification of Proteins database","level":3,"score":0.4882564842700958},{"id":"https://openalex.org/C136475424","wikidata":"https://www.wikidata.org/wiki/Q7251500","display_name":"Protein structure database","level":4,"score":0.48781922459602356},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4718988835811615},{"id":"https://openalex.org/C144292202","wikidata":"https://www.wikidata.org/wiki/Q898273","display_name":"Protein domain","level":3,"score":0.46431538462638855},{"id":"https://openalex.org/C165525559","wikidata":"https://www.wikidata.org/wiki/Q224180","display_name":"Homology (biology)","level":3,"score":0.45870646834373474},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4501205086708069},{"id":"https://openalex.org/C45475804","wikidata":"https://www.wikidata.org/wiki/Q6675846","display_name":"Loop modeling","level":4,"score":0.42328715324401855},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.3065311312675476},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.2418023943901062},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1816832423210144},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1331779658794403},{"id":"https://openalex.org/C41584329","wikidata":"https://www.wikidata.org/wiki/Q175902","display_name":"Sequence database","level":3,"score":0.11077404022216797},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.10378941893577576},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.09966546297073364},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","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},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/ipdps.2006.1639540","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ipdps.2006.1639540","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings 20th IEEE International Parallel & Distributed Processing Symposium","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":26,"referenced_works":["https://openalex.org/W1508885706","https://openalex.org/W1980374511","https://openalex.org/W2002638840","https://openalex.org/W2004228538","https://openalex.org/W2013136212","https://openalex.org/W2017727500","https://openalex.org/W2022366078","https://openalex.org/W2026258231","https://openalex.org/W2030750720","https://openalex.org/W2042516820","https://openalex.org/W2062693912","https://openalex.org/W2106882534","https://openalex.org/W2108401170","https://openalex.org/W2111373249","https://openalex.org/W2114520383","https://openalex.org/W2125725297","https://openalex.org/W2127122014","https://openalex.org/W2136297983","https://openalex.org/W2140455347","https://openalex.org/W2149480059","https://openalex.org/W2151831732","https://openalex.org/W2152326664","https://openalex.org/W2161896699","https://openalex.org/W2163105490","https://openalex.org/W2170666908","https://openalex.org/W4210400672"],"related_works":["https://openalex.org/W2099254366","https://openalex.org/W646353556","https://openalex.org/W161814595","https://openalex.org/W2902750099","https://openalex.org/W1643430841","https://openalex.org/W2131204071","https://openalex.org/W2125800162","https://openalex.org/W1997379747","https://openalex.org/W4232453105","https://openalex.org/W2106883599"],"abstract_inverted_index":{"Homology":[0],"modeling":[1,20,77],"requires":[2],"an":[3],"accurate":[4],"alignment":[5,117,142,182],"between":[6,144],"a":[7,72,114,145,192],"query":[8,146,159],"sequence":[9,36],"and":[10,51,86,98,147,150,179],"its":[11,148],"homologs":[12],"with":[13,38,198],"known":[14,58,195],"three-dimensional":[15],"(3D)":[16],"information.":[17],"Current":[18],"structural":[19,76,116,135],"techniques":[21],"largely":[22,44],"use":[23],"entire":[24,95],"protein":[25,59,66,196],"chains":[26],"as":[27,46,137],"templates,":[28,149],"which":[29],"are":[30],"selected":[31],"based":[32,78,120],"only":[33,121],"on":[34,79,122,165],"their":[35],"alignments":[37,136],"the":[39,57,65,89,94,103,110,123,128,134,141,153,163,180,188],"queries.":[40],"Protein":[41],"can":[42,61,184],"be":[43,62,185],"described":[45],"combinations":[47],"of":[48,56,109,126,155,194],"conserved":[49,80],"domains,":[50],"already":[52],"more":[53],"than":[54],"two-third":[55],"domains":[60,92,101],"found":[63],"in":[64,93],"data":[67],"bank":[68],"(PDB).":[69],"We":[70,161],"presented":[71],"method":[73,164],"to":[74,139],"improve":[75,152],"domain":[81],"clusters.":[82],"First,":[83],"we":[84,132],"searched":[85],"mapped":[87],"all":[88,127],"inter":[90],"pro":[91],"PDB,":[96],"partitioned":[97],"clustered":[99],"homologous":[100],"into":[102],"domain-based":[104,176],"template":[105,177],"library.":[106],"For":[107],"each":[108],"resulting":[111],"clusters":[112],"created,":[113],"multiple":[115],"was":[118],"generated":[119],"3D":[124],"coordinates":[125],"residues":[129],"involved.":[130],"Then":[131],"used":[133,186],"anchors":[138],"increase":[140],"accuracy":[143],"consequently":[151],"quality":[154],"predicted":[156],"structure":[157],"for":[158,187,191],"protein.":[160],"implemented":[162],"DAWNING":[166],"4000A":[167],"cluster":[168],"system.":[169],"The":[170],"preliminary":[171],"results":[172],"show":[173],"that":[174],"our":[175],"library":[178],"structure-anchored":[181],"protocol":[183],"partial":[189],"prediction":[190],"majority":[193],"sequences":[197],"better":[199],"qualities.":[200]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}