{"id":"https://openalex.org/W2972577708","doi":"https://doi.org/10.1145/3307339.3343243","title":"Contact-assisted Protein Threading","display_name":"Contact-assisted Protein Threading","publication_year":2019,"publication_date":"2019-09-04","ids":{"openalex":"https://openalex.org/W2972577708","doi":"https://doi.org/10.1145/3307339.3343243","mag":"2972577708"},"language":"en","primary_location":{"id":"doi:10.1145/3307339.3343243","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3307339.3343243","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","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/A5101844843","display_name":"Sutanu Bhattacharya","orcid":"https://orcid.org/0000-0002-3780-5174"},"institutions":[{"id":"https://openalex.org/I82497590","display_name":"Auburn University","ror":"https://ror.org/02v80fc35","country_code":"US","type":"education","lineage":["https://openalex.org/I82497590"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sutanu Bhattacharya","raw_affiliation_strings":["Auburn University, Auburn, AL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Auburn University, Auburn, AL, USA","institution_ids":["https://openalex.org/I82497590"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5018409409","display_name":"Debswapna Bhattacharya","orcid":"https://orcid.org/0000-0002-9630-0141"},"institutions":[{"id":"https://openalex.org/I82497590","display_name":"Auburn University","ror":"https://ror.org/02v80fc35","country_code":"US","type":"education","lineage":["https://openalex.org/I82497590"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Debswapna Bhattacharya","raw_affiliation_strings":["Auburn University, Auburn, AL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Auburn University, Auburn, AL, USA","institution_ids":["https://openalex.org/I82497590"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I82497590"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.08329671,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"536","last_page":"536"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.996999979019165,"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":0.996999979019165,"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/T10260","display_name":"Software Engineering Research","score":0.9596999883651733,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T13326","display_name":"Biochemical and Structural Characterization","score":0.9251999855041504,"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/threading","display_name":"Threading (protein sequence)","score":0.9581841230392456},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.7113012671470642},{"id":"https://openalex.org/keywords/template","display_name":"Template","score":0.6176356077194214},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5899639129638672},{"id":"https://openalex.org/keywords/casp","display_name":"CASP","score":0.5059835314750671},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.47217077016830444},{"id":"https://openalex.org/keywords/ab-initio","display_name":"Ab initio","score":0.4160895347595215},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.3629555404186249},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3324856758117676},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.32698291540145874},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3202248215675354},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11390578746795654},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.10097554326057434}],"concepts":[{"id":"https://openalex.org/C200307862","wikidata":"https://www.wikidata.org/wiki/Q7797175","display_name":"Threading (protein sequence)","level":3,"score":0.9581841230392456},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.7113012671470642},{"id":"https://openalex.org/C82714645","wikidata":"https://www.wikidata.org/wiki/Q438331","display_name":"Template","level":2,"score":0.6176356077194214},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5899639129638672},{"id":"https://openalex.org/C66153294","wikidata":"https://www.wikidata.org/wiki/Q899291","display_name":"CASP","level":4,"score":0.5059835314750671},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.47217077016830444},{"id":"https://openalex.org/C2781442258","wikidata":"https://www.wikidata.org/wiki/Q46310","display_name":"Ab initio","level":2,"score":0.4160895347595215},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.3629555404186249},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3324856758117676},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.32698291540145874},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3202248215675354},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11390578746795654},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.10097554326057434},{"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/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","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":1,"locations":[{"id":"doi:10.1145/3307339.3343243","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3307339.3343243","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2411998238","https://openalex.org/W2462594639","https://openalex.org/W2117340986","https://openalex.org/W2335447195","https://openalex.org/W2159298533","https://openalex.org/W2113993025","https://openalex.org/W2098138211","https://openalex.org/W2946599741","https://openalex.org/W2136856901","https://openalex.org/W1888349473"],"abstract_inverted_index":{"Protein":[0],"threading":[1,46,63,71,94,108,131,165,182,188,200,224,228,248,280,295,323,369],"is":[2,331,379],"a":[3,43,327,361],"popular":[4,107],"template-based":[5],"approach":[6],"for":[7],"predicting":[8],"protein":[9,164,238,375],"three-dimensional":[10],"structure":[11],"in":[12,29,354],"the":[13,75,112,144,172,176,219,226,231,276,285,299,315,321,343,351,371],"absence":[14],"of":[15,77,178,237,257,266,275,288,306,350,364,373],"close":[16],"templates.":[17],"However,":[18],"identifying":[19,267],"remote":[20],"homologous":[21],"templates":[22],"remains":[23],"challenging.":[24],"Inspired":[25],"by":[26,34,184,325],"recent":[27],"progress":[28],"inter-residue":[30],"contact":[31,53,152,161,179,292,304,317,345,355],"prediction":[32,356],"driven":[33],"sequence":[35],"co-evolution":[36],"and":[37,59,119,181,196,208,251],"deep":[38],"learning,":[39],"we":[40,297],"have":[41],"developed":[42],"new":[44],"contact-assisted":[45,104,130,136,187,247,279,368],"method":[47,95,105,109,132,140,272],"to":[48,91,204,283,333],"explore":[49],"whether":[50],"incorporating":[51,159],"residue-residue":[52,160],"information":[54],"along":[55],"with":[56,74,214,217],"various":[57],"sequential":[58],"structural":[60],"features":[61],"improves":[62],"performance":[64,72,183,201,324],"[1].":[65],"Experimental":[66],"results":[67,156,312],"show":[68],"statistically":[69,339],"significant":[70],"boost":[73,163],"incorporation":[76],"native":[78],"contacts":[79,89,194,206],"as":[80,82,202,261,263,273],"well":[81,262],"ultra-deep":[83],"learning":[84,213],"based":[85,149,193,253],"state-of-the-art":[86,246,291],"RaptorX":[87],"predicted":[88,120,151],"compared":[90],"baseline":[92],"contact-free":[93],"on":[96,111,124,254,294],"Test500":[97],"dataset.":[98],"We":[99],"also":[100],"observe":[101],"that":[102,128,158,186,210,314,330],"our":[103,129,168,243,271],"outperforms":[106,134,245],"MUSTER":[110],"same":[113,145],"dataset":[114,126],"(Test500)":[115],"using":[116,143,189],"both":[117,142],"true":[118],"contacts.":[121],"Furthermore,":[122,167,282],"benchmarking":[123],"PSICOV150":[125],"reveals":[127],"significantly":[133,340],"cutting-edge":[135,278],"ab":[137],"initio":[138],"folding":[139],"CONFOLD2,":[141],"classical":[146],"neural":[147],"network":[148],"MetaPSICOV":[150],"maps.":[153],"Overall,":[154],"these":[155],"demonstrate":[157,313],"maps":[162,180,293],"performance.":[166,229],"systematic":[169],"study":[170,359],"unravels":[171],"mutual":[173],"association":[174],"between":[175],"quality":[177],"demonstrating":[185],"low-quality":[190],"pure":[191],"co-evolutionary":[192,215],"(mfDCA":[195],"PSICOV)":[197],"badly":[198],"degrades":[199],"opposed":[203],"high-quality":[205],"(RaptorX":[207],"MetaPSICOV)":[209],"combine":[211],"machine":[212],"information,":[216],"RaptorX,":[218],"most":[220],"accurate":[221,290],"contacts,":[222],"assisted":[223],"attaining":[225],"best":[227,277,322],"On":[230],"recently":[232],"concluded":[233],"13th":[234],"Critical":[235],"Assessment":[236],"Structure":[239],"Prediction":[240],"(CASP13)":[241],"experiment,":[242],"work":[244],"methods":[249],"EigenThreader":[250],"map_align":[252],"mean":[255,328],"TM-score":[256,329],"top":[258,300,335],"ranked":[259,303,336],"models":[260],"success":[264],"rate":[265],"correct":[268],"folds,":[269],"establishing":[270],"one":[274],"methods.":[281],"investigate":[284],"relative":[286],"contribution":[287],"highly":[289],"performance,":[296],"consider":[298],"five":[301],"officially":[302],"predictors":[305],"comparable":[307,332],"qualities":[308],"from":[309],"CASP13.":[310],"The":[311],"first-ranked":[316],"predictor,":[318,346],"TripletRes,":[319],"attains":[320],"reaching":[326],"other":[334],"predictors,":[337],"but":[338],"better":[341],"than":[342],"fifth-ranked":[344],"DeepMetaPSICOV.":[347],"In":[348],"view":[349],"rapid":[352],"developments":[353],"technologies,":[357],"this":[358],"opens":[360],"fertile":[362],"line":[363],"research":[365],"-":[366],"how":[367],"pushes":[370],"frontier":[372],"low-homology":[374],"modeling":[376],"beyond":[377],"what":[378],"currently":[380],"feasible.":[381]},"counts_by_year":[{"year":2024,"cited_by_count":1}],"updated_date":"2026-06-26T08:34:08.712188","created_date":"2025-10-10T00:00:00"}
