{"id":"https://openalex.org/W3004824892","doi":"https://doi.org/10.1109/bibm47256.2019.8983080","title":"MUFold-Contact and TPCref: New Methods for Protein Structure Contact Prediction and Refinement","display_name":"MUFold-Contact and TPCref: New Methods for Protein Structure Contact Prediction and Refinement","publication_year":2019,"publication_date":"2019-11-01","ids":{"openalex":"https://openalex.org/W3004824892","doi":"https://doi.org/10.1109/bibm47256.2019.8983080","mag":"3004824892"},"language":"en","primary_location":{"id":"doi:10.1109/bibm47256.2019.8983080","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm47256.2019.8983080","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","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/A5014624926","display_name":"Jeffrey A. Ruffolo","orcid":"https://orcid.org/0000-0002-3385-9191"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jeffrey Ruffolo","raw_affiliation_strings":["University of Missouri,Department of EECS,Columbia,MO,USA","Department of EECS, University of Missouri, Columbia, MO, USA"],"affiliations":[{"raw_affiliation_string":"University of Missouri,Department of EECS,Columbia,MO,USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Department of EECS, University of Missouri, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100726724","display_name":"Zhaoyu Li","orcid":"https://orcid.org/0000-0002-1136-2758"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhaoyu Li","raw_affiliation_strings":["University of Missouri,Department of EECS,Columbia,MO,USA","Department of EECS, University of Missouri, Columbia, MO, USA"],"affiliations":[{"raw_affiliation_string":"University of Missouri,Department of EECS,Columbia,MO,USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Department of EECS, University of Missouri, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5057883374","display_name":"Yi Shang","orcid":"https://orcid.org/0000-0001-7771-4034"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yi Shang","raw_affiliation_strings":["University of Missouri,Department of EECS,Columbia,MO,USA","Department of EECS, University of Missouri, Columbia, MO, USA"],"affiliations":[{"raw_affiliation_string":"University of Missouri,Department of EECS,Columbia,MO,USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Department of EECS, University of Missouri, Columbia, MO, USA","institution_ids":["https://openalex.org/I76835614"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5014624926"],"corresponding_institution_ids":["https://openalex.org/I76835614"],"apc_list":null,"apc_paid":null,"fwci":0.0852,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.48860534,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"90","last_page":"93"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9994000196456909,"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":0.9994000196456909,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9864000082015991,"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/T13326","display_name":"Biochemical and Structural Characterization","score":0.9812999963760376,"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/template","display_name":"Template","score":0.642379641532898},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.5948420166969299},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5539238452911377},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.5462134480476379},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5321432948112488},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.43994051218032837},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3689335584640503},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.2891809344291687},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.08087864518165588}],"concepts":[{"id":"https://openalex.org/C82714645","wikidata":"https://www.wikidata.org/wiki/Q438331","display_name":"Template","level":2,"score":0.642379641532898},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.5948420166969299},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5539238452911377},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.5462134480476379},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5321432948112488},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.43994051218032837},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3689335584640503},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.2891809344291687},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.08087864518165588},{"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}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm47256.2019.8983080","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm47256.2019.8983080","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","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":20,"referenced_works":["https://openalex.org/W1540530720","https://openalex.org/W2008545402","https://openalex.org/W2013425283","https://openalex.org/W2015470526","https://openalex.org/W2033354942","https://openalex.org/W2060107523","https://openalex.org/W2107517961","https://openalex.org/W2114340287","https://openalex.org/W2120836664","https://openalex.org/W2136799255","https://openalex.org/W2137566700","https://openalex.org/W2137965757","https://openalex.org/W2153153865","https://openalex.org/W2280207768","https://openalex.org/W2395611524","https://openalex.org/W2600704321","https://openalex.org/W2625681382","https://openalex.org/W2942618964","https://openalex.org/W2944535254","https://openalex.org/W2971003495"],"related_works":["https://openalex.org/W2121300814","https://openalex.org/W4231091074","https://openalex.org/W1886613375","https://openalex.org/W4236081792","https://openalex.org/W4250583430","https://openalex.org/W4234406076","https://openalex.org/W2010731026","https://openalex.org/W3023334178","https://openalex.org/W2036923798","https://openalex.org/W2113993025"],"abstract_inverted_index":{"When":[0],"predicting":[1,43],"proteins'":[2],"3-D":[3],"structures":[4,122],"from":[5,46],"their":[6],"primary":[7],"sequences,":[8,48],"many":[9],"existing":[10,184],"tools":[11],"use":[12,93,119],"predicted":[13,126,147],"residue":[14,85],"contact":[15,22,45,57,98,104,127,148,180],"information,":[16],"i.e.":[17],"which":[18,140],"residues":[19],"are":[20],"in":[21,74],"with":[23,169],"each":[24],"other.":[25],"In":[26],"this":[27],"paper,":[28],"we":[29],"propose":[30],"two":[31],"new":[32,36],"methods:":[33],"MUFold-Contact,":[34],"a":[35,56,89,102,136],"two-stage":[37],"multi-branch":[38],"deep":[39,67,80],"neural":[40,68,81],"network":[41,82],"for":[42,51],"structure":[44],"protein":[47,94],"and":[49,118,123],"TPCref":[50,87,176],"refining":[52],"the":[53,115,120,124,131,146,151,163,172,179],"result":[54],"of":[55,150,165,171,183],"prediction":[58,99,105,181],"tool":[59],"using":[60,156],"template":[61,111],"information.":[62],"MUFold-Contact":[63,166],"uses":[64],"four":[65],"independently-trained":[66],"networks":[69],"to":[70,83,92,96,134,144],"predict":[71,84],"residue-residue":[72],"distances":[73],"various":[75],"ranges,":[76],"followed":[77],"by":[78,101,130],"one":[79],"contact.":[86],"is":[88,141],"novel":[90],"approach":[91],"templates":[95],"refine":[97,145],"generated":[100,129],"particular":[103],"method.":[106],"It":[107],"first":[108],"finds":[109],"multiple":[110],"sequences":[112],"based":[113],"on":[114],"target":[116,137,152],"sequence,":[117],"templates'":[121,125],"map":[128,149],"contact-prediction":[132],"method":[133],"form":[135],"contact-map":[138],"filter,":[139],"then":[142],"used":[143],"sequence.":[153],"Experimental":[154],"results":[155,182],"recently":[157],"released":[158],"PDB":[159],"proteins":[160],"show":[161],"that":[162],"performance":[164],"was":[167],"comparable":[168],"those":[170],"state-of-the-art":[173],"methods,":[174],"while":[175],"significantly":[177],"improved":[178],"methods.":[185]},"counts_by_year":[{"year":2020,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}