{"id":"https://openalex.org/W2127512100","doi":"https://doi.org/10.1109/bibe.2003.1188923","title":"A computational pipeline for protein structure prediction and analysis at genome scale","display_name":"A computational pipeline for protein structure prediction and analysis at genome scale","publication_year":2003,"publication_date":"2003-11-21","ids":{"openalex":"https://openalex.org/W2127512100","doi":"https://doi.org/10.1109/bibe.2003.1188923","mag":"2127512100"},"language":"en","primary_location":{"id":"doi:10.1109/bibe.2003.1188923","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2003.1188923","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Third IEEE Symposium on Bioinformatics and Bioengineering, 2003. Proceedings.","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/A5035410248","display_name":"Manesh Shah","orcid":"https://orcid.org/0000-0003-1436-5345"},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"M. Shah","raw_affiliation_strings":["Oak Ridge National Laboratory, Oak Ridge, TN, US","Life Sci. Div., Oak Ridge Nat. Lab., TN, USA"],"affiliations":[{"raw_affiliation_string":"Oak Ridge National Laboratory, Oak Ridge, TN, US","institution_ids":["https://openalex.org/I1289243028"]},{"raw_affiliation_string":"Life Sci. Div., Oak Ridge Nat. Lab., TN, USA","institution_ids":["https://openalex.org/I1289243028"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048405797","display_name":"Sergei Passovets","orcid":null},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"S. Passovets","raw_affiliation_strings":["Oak Ridge National Laboratory, Oak Ridge, TN, US","Life Sci. Div., Oak Ridge Nat. Lab., TN, USA"],"affiliations":[{"raw_affiliation_string":"Oak Ridge National Laboratory, Oak Ridge, TN, US","institution_ids":["https://openalex.org/I1289243028"]},{"raw_affiliation_string":"Life Sci. Div., Oak Ridge Nat. Lab., TN, USA","institution_ids":["https://openalex.org/I1289243028"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071721971","display_name":"Dongsup Kim","orcid":"https://orcid.org/0000-0002-5916-6799"},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dongsup Kim","raw_affiliation_strings":["Life Sci. Div., Oak Ridge Nat. Lab., TN, USA"],"affiliations":[{"raw_affiliation_string":"Life Sci. Div., Oak Ridge Nat. Lab., TN, USA","institution_ids":["https://openalex.org/I1289243028"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055055227","display_name":"Kyle Ellrott","orcid":"https://orcid.org/0000-0002-6573-5900"},"institutions":[{"id":"https://openalex.org/I75027704","display_name":"University of Tennessee at Knoxville","ror":"https://ror.org/020f3ap87","country_code":"US","type":"education","lineage":["https://openalex.org/I75027704"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"K. Ellrott","raw_affiliation_strings":["University of Tennessee Knoxville"],"affiliations":[{"raw_affiliation_string":"University of Tennessee Knoxville","institution_ids":["https://openalex.org/I75027704"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100336185","display_name":"L\u0131 Wang","orcid":"https://orcid.org/0000-0003-1688-064X"},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]},{"id":"https://openalex.org/I75027704","display_name":"University of Tennessee at Knoxville","ror":"https://ror.org/020f3ap87","country_code":"US","type":"education","lineage":["https://openalex.org/I75027704"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Li Wang","raw_affiliation_strings":["Oak Ridge National Laboratory","University of Tennessee, Knoxville"],"affiliations":[{"raw_affiliation_string":"Oak Ridge National Laboratory","institution_ids":["https://openalex.org/I1289243028"]},{"raw_affiliation_string":"University of Tennessee, Knoxville","institution_ids":["https://openalex.org/I75027704"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5028839663","display_name":"Inna Vokler","orcid":null},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]},{"id":"https://openalex.org/I75027704","display_name":"University of Tennessee at Knoxville","ror":"https://ror.org/020f3ap87","country_code":"US","type":"education","lineage":["https://openalex.org/I75027704"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"I. Vokler","raw_affiliation_strings":["Oak Ridge National Laboratory","University of Tennessee, Knoxville"],"affiliations":[{"raw_affiliation_string":"Oak Ridge National Laboratory","institution_ids":["https://openalex.org/I1289243028"]},{"raw_affiliation_string":"University of Tennessee, Knoxville","institution_ids":["https://openalex.org/I75027704"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5035410248"],"corresponding_institution_ids":["https://openalex.org/I1289243028"],"apc_list":null,"apc_paid":null,"fwci":0.2288,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.54273493,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"253","issue":null,"first_page":"3","last_page":"10"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9983000159263611,"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":0.9983000159263611,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9977999925613403,"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":0.996999979019165,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.8014468550682068},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6899561882019043},{"id":"https://openalex.org/keywords/threading","display_name":"Threading (protein sequence)","score":0.6297823786735535},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6118758320808411},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.4365101456642151},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.42848584055900574},{"id":"https://openalex.org/keywords/protein-structure-database","display_name":"Protein structure database","score":0.42765721678733826},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.4228164851665497},{"id":"https://openalex.org/keywords/caenorhabditis-elegans","display_name":"Caenorhabditis elegans","score":0.4212588369846344},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.4110785722732544},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.33704283833503723},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3268318176269531},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2398504614830017},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.15850785374641418},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13544633984565735},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13095632195472717}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.8014468550682068},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6899561882019043},{"id":"https://openalex.org/C200307862","wikidata":"https://www.wikidata.org/wiki/Q7797175","display_name":"Threading (protein sequence)","level":3,"score":0.6297823786735535},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6118758320808411},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.4365101456642151},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.42848584055900574},{"id":"https://openalex.org/C136475424","wikidata":"https://www.wikidata.org/wiki/Q7251500","display_name":"Protein structure database","level":4,"score":0.42765721678733826},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.4228164851665497},{"id":"https://openalex.org/C2778944004","wikidata":"https://www.wikidata.org/wiki/Q91703","display_name":"Caenorhabditis elegans","level":3,"score":0.4212588369846344},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4110785722732544},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.33704283833503723},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3268318176269531},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2398504614830017},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.15850785374641418},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13544633984565735},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13095632195472717},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","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},{"id":"https://openalex.org/C41584329","wikidata":"https://www.wikidata.org/wiki/Q175902","display_name":"Sequence database","level":3,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1109/bibe.2003.1188923","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2003.1188923","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Third IEEE Symposium on Bioinformatics and Bioengineering, 2003. Proceedings.","raw_type":"proceedings-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.153.1021","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.153.1021","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oupjournals.org/cgi/reprint/19/15/1985.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.563.5697","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.563.5697","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/19/15/1985.full.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.98.3654","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.98.3654","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.genomes2life.org/publications/comp-pipeline.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320310010","display_name":"University of Georgia","ror":"https://ror.org/00te3t702"},{"id":"https://openalex.org/F4320338287","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W1524556134","https://openalex.org/W1972436355","https://openalex.org/W1994025789","https://openalex.org/W2005038007","https://openalex.org/W2011495938","https://openalex.org/W2016411902","https://openalex.org/W2020588471","https://openalex.org/W2024645073","https://openalex.org/W2028843689","https://openalex.org/W2033496784","https://openalex.org/W2035033944","https://openalex.org/W2055043387","https://openalex.org/W2065117679","https://openalex.org/W2065283382","https://openalex.org/W2066468520","https://openalex.org/W2083445888","https://openalex.org/W2085277871","https://openalex.org/W2105840826","https://openalex.org/W2107643343","https://openalex.org/W2117919289","https://openalex.org/W2127230663","https://openalex.org/W2129421547","https://openalex.org/W2132717858","https://openalex.org/W2139621307","https://openalex.org/W2141885858","https://openalex.org/W2147737262","https://openalex.org/W2147809382","https://openalex.org/W2152770371","https://openalex.org/W2153187042","https://openalex.org/W2158714788","https://openalex.org/W2166278492","https://openalex.org/W2168909179","https://openalex.org/W2171091522"],"related_works":["https://openalex.org/W2253761889","https://openalex.org/W1741740882","https://openalex.org/W2181585194","https://openalex.org/W3149404221","https://openalex.org/W646353556","https://openalex.org/W2136856901","https://openalex.org/W1504467230","https://openalex.org/W4311623193","https://openalex.org/W2043066834","https://openalex.org/W2398461637"],"abstract_inverted_index":{"Traditionally,":[0],"protein":[1,27,51,57,83,94],"3D":[2],"structures":[3],"are":[4],"solved":[5],"using":[6],"experimental":[7,19,72],"techniques,":[8],"like":[9],"X-ray":[10],"crystallography":[11],"or":[12],"nuclear":[13],"magnetic":[14],"resonance":[15],"(NMR).":[16],"While":[17],"these":[18],"techniques":[20,55],"have":[21,60,102,146],"been":[22,103,124,147],"the":[23,31,47,70,89,106],"main":[24],"workhorse":[25],"for":[26,56,82,105],"structure":[28,58,84,95],"studies":[29],"in":[30,128],"past":[32,107],"few":[33,108],"decades,":[34],"it":[35],"is":[36,91],"becoming":[37],"increasingly":[38],"apparent":[39],"that":[40,66],"they":[41,67],"alone":[42],"cannot":[43],"keep":[44],"up":[45],"with":[46,137],"production":[48],"rate":[49],"of":[50,88,113,143],"sequences.":[52],"Fortunately,":[53],"computational":[54,131],"predictions":[59],"matured":[61],"to":[62,126],"such":[63],"a":[64,92,118,129,134,138],"level":[65],"can":[68],"complement":[69],"existing":[71],"techniques.":[73],"In":[74],"this":[75],"paper,":[76],"we":[77,101,154],"present":[78,155],"an":[79],"automated":[80],"pipeline":[81,90,111,122],"prediction.":[85],"The":[86,110,121],"centerpiece":[87],"threading-based":[93],"prediction":[96],"system,":[97],"called":[98],"PROSPECT,":[99],"which":[100],"developing":[104],"years.":[109],"consists":[112],"seven":[114],"logical":[115],"phases,":[116],"utilizing":[117],"dozen":[119],"tools.":[120],"has":[123],"implemented":[125],"run":[127],"heterogeneous":[130],"environment":[132],"as":[133],"client/server":[135],"system":[136],"web":[139],"interface.":[140],"A":[141],"number":[142],"genome-scale":[144,157],"applications":[145],"carried":[148],"out":[149],"on":[150,159],"microbial":[151],"genomes.":[152],"Here":[153],"one":[156],"application":[158],"Caenorhabditis":[160],"elegans.":[161]},"counts_by_year":[],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}