{"id":"https://openalex.org/W4400275215","doi":"https://doi.org/10.1109/tcbb.2024.3422288","title":"AnglesRefine: Refinement of 3D Protein Structures Using Transformer Based on Torsion Angles","display_name":"AnglesRefine: Refinement of 3D Protein Structures Using Transformer Based on Torsion Angles","publication_year":2024,"publication_date":"2024-07-03","ids":{"openalex":"https://openalex.org/W4400275215","doi":"https://doi.org/10.1109/tcbb.2024.3422288","pmid":"https://pubmed.ncbi.nlm.nih.gov/38959143"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2024.3422288","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2024.3422288","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5080798381","display_name":"Lei Zhang","orcid":"https://orcid.org/0000-0002-6447-2053"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lei Zhang","raw_affiliation_strings":["Information Materials and Intelligent Sensing Laboratory of Anhui Province, School of Computer Science and Technology, Anhui University, Hefei, China"],"raw_orcid":"https://orcid.org/0000-0002-6447-2053","affiliations":[{"raw_affiliation_string":"Information Materials and Intelligent Sensing Laboratory of Anhui Province, School of Computer Science and Technology, Anhui University, Hefei, China","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041347085","display_name":"Junyong Zhu","orcid":"https://orcid.org/0000-0002-1200-715X"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Junyong Zhu","raw_affiliation_strings":["Information Materials and Intelligent Sensing Laboratory of Anhui Province, School of Computer Science and Technology, Anhui University, Hefei, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Information Materials and Intelligent Sensing Laboratory of Anhui Province, School of Computer Science and Technology, Anhui University, Hefei, China","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100371318","display_name":"Sheng Wang","orcid":"https://orcid.org/0000-0003-3537-1680"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Sheng Wang","raw_affiliation_strings":["Information Materials and Intelligent Sensing Laboratory of Anhui Province, School of Computer Science and Technology, Anhui University, Hefei, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Information Materials and Intelligent Sensing Laboratory of Anhui Province, School of Computer Science and Technology, Anhui University, Hefei, China","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022495891","display_name":"Jie Hou","orcid":"https://orcid.org/0000-0002-8584-5154"},"institutions":[{"id":"https://openalex.org/I47838141","display_name":"Saint Louis University","ror":"https://ror.org/01p7jjy08","country_code":"US","type":"education","lineage":["https://openalex.org/I47838141"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jie Hou","raw_affiliation_strings":["Department of Computer Science, Saint Louis University, St. Louis, MO, USA","Department of Computer Science, Saint Louis University, Saint. Louis, MO, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Saint Louis University, St. Louis, MO, USA","institution_ids":["https://openalex.org/I47838141"]},{"raw_affiliation_string":"Department of Computer Science, Saint Louis University, Saint. Louis, MO, USA","institution_ids":["https://openalex.org/I47838141"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080683855","display_name":"Dong Si","orcid":"https://orcid.org/0000-0001-7039-2589"},"institutions":[{"id":"https://openalex.org/I4210138624","display_name":"University of Washington Bothell","ror":"https://ror.org/02ygzhr13","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701","https://openalex.org/I4210138624"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dong Si","raw_affiliation_strings":["School of Computing and Software, Washington Bothell University, Bothell, WA, USA"],"raw_orcid":"https://orcid.org/0000-0001-7039-2589","affiliations":[{"raw_affiliation_string":"School of Computing and Software, Washington Bothell University, Bothell, WA, USA","institution_ids":["https://openalex.org/I4210138624"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085487073","display_name":"Renzhi Cao","orcid":"https://orcid.org/0000-0002-8345-343X"},"institutions":[{"id":"https://openalex.org/I60065076","display_name":"Pacific Lutheran University","ror":"https://ror.org/01vh5nd96","country_code":"US","type":"education","lineage":["https://openalex.org/I60065076"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Renzhi Cao","raw_affiliation_strings":["School of Computer Science, Pacific Lutheran University, Tacoma, WA, USA"],"raw_orcid":"https://orcid.org/0000-0002-8345-343X","affiliations":[{"raw_affiliation_string":"School of Computer Science, Pacific Lutheran University, Tacoma, WA, USA","institution_ids":["https://openalex.org/I60065076"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.03667954,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"2","first_page":"397","last_page":"408"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9455000162124634,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9455000162124634,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T10885","display_name":"Gene expression and cancer classification","score":0.9258999824523926,"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/torsion","display_name":"Torsion (gastropod)","score":0.6603028774261475},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.5422447919845581},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.44720447063446045},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.34595388174057007},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.32039982080459595},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.25850677490234375},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.19201192259788513},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1472095549106598},{"id":"https://openalex.org/keywords/electrical-engineering","display_name":"Electrical engineering","score":0.14139902591705322},{"id":"https://openalex.org/keywords/anatomy","display_name":"Anatomy","score":0.13234871625900269},{"id":"https://openalex.org/keywords/voltage","display_name":"Voltage","score":0.056137800216674805}],"concepts":[{"id":"https://openalex.org/C77461463","wikidata":"https://www.wikidata.org/wiki/Q7827201","display_name":"Torsion (gastropod)","level":2,"score":0.6603028774261475},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.5422447919845581},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.44720447063446045},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.34595388174057007},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.32039982080459595},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.25850677490234375},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.19201192259788513},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1472095549106598},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.14139902591705322},{"id":"https://openalex.org/C105702510","wikidata":"https://www.wikidata.org/wiki/Q514","display_name":"Anatomy","level":1,"score":0.13234871625900269},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.056137800216674805}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2024.3422288","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2024.3422288","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38959143","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38959143","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6658230062","display_name":null,"funder_award_id":"61976001","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":32,"referenced_works":["https://openalex.org/W1785767033","https://openalex.org/W1998917415","https://openalex.org/W2110483430","https://openalex.org/W2139915497","https://openalex.org/W2140673705","https://openalex.org/W2142529984","https://openalex.org/W2142678478","https://openalex.org/W2151581834","https://openalex.org/W2158562723","https://openalex.org/W2912932504","https://openalex.org/W2937569020","https://openalex.org/W2949975032","https://openalex.org/W2954994557","https://openalex.org/W2963212560","https://openalex.org/W2987451562","https://openalex.org/W2997234557","https://openalex.org/W3095717210","https://openalex.org/W3101509328","https://openalex.org/W3132153121","https://openalex.org/W3159634588","https://openalex.org/W3159717976","https://openalex.org/W3162037110","https://openalex.org/W3163965514","https://openalex.org/W3175014854","https://openalex.org/W3177828909","https://openalex.org/W3184540805","https://openalex.org/W3186179742","https://openalex.org/W3196411235","https://openalex.org/W4313430582","https://openalex.org/W4372331183","https://openalex.org/W4385245566","https://openalex.org/W6790349137"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W4246450666","https://openalex.org/W4388998267","https://openalex.org/W2898370298","https://openalex.org/W2137437058","https://openalex.org/W4396520874","https://openalex.org/W4390401159","https://openalex.org/W2744391499","https://openalex.org/W2103929723"],"abstract_inverted_index":{"The":[0],"goal":[1],"of":[2,11,20,147,155],"protein":[3,13,52,58,80,93],"structure":[4,53,59,73,81],"refinement":[5,25,188],"is":[6,158],"to":[7,47,55,77,186],"enhance":[8],"the":[9,17,21,97,109,125,136,144,152,173],"precision":[10],"predicted":[12],"models,":[14],"particularly":[15],"at":[16],"residue":[18],"level":[19],"local":[22],"structure.":[23],"Existing":[24],"approaches":[26],"primarily":[27],"rely":[28],"on":[29,69,96,124,135],"physics,":[30],"whereas":[31],"molecular":[32],"simulation":[33],"methods":[34,46,107,164],"are":[35,165],"resource-intensive":[36],"and":[37,74,111,178],"time-consuming.":[38],"In":[39],"this":[40],"study,":[41],"we":[42],"employ":[43],"deep":[44],"learning":[45],"extract":[48],"structural":[49],"constraints":[50],"from":[51],"residues":[54],"assist":[56],"in":[57],"refinement.":[60],"We":[61,100],"introduce":[62],"a":[63,70,91],"novel":[64],"method,":[65],"AnglesRefine,":[66],"which":[67],"focuses":[68],"protein's":[71],"secondary":[72],"employs":[75],"transformer":[76],"refine":[78],"various":[79],"angles":[82],"(psi,":[83],"phi,":[84],"omega,":[85],"CA_C_N_angle,":[86],"C_N_CA_angle,":[87],"N_CA_C_angle),":[88],"ultimately":[89],"generating":[90],"superior":[92],"model":[94,148],"based":[95],"refined":[98],"angles.":[99],"evaluate":[101],"our":[102,118,156,170],"approach":[103,171],"against":[104],"other":[105,122,163],"cutting-edge":[106],"using":[108],"CASP11-14":[110,126],"CASP15":[112,137],"datasets.":[113],"Experimental":[114],"outcomes":[115],"indicate":[116],"that":[117],"method":[119,141,157],"generally":[120],"surpasses":[121],"techniques":[123],"test":[127,138],"dataset,":[128],"while":[129,162],"performing":[130],"comparably":[131],"or":[132],"marginally":[133],"better":[134],"dataset.":[139],"Our":[140],"consistently":[142],"demonstrates":[143],"least":[145],"likelihood":[146],"quality":[149],"degradation,":[150],"e.g.,":[151],"degradation":[153],"percentage":[154],"less":[159],"than":[160],"10%,":[161],"about":[166],"50%.":[167],"Furthermore,":[168],"as":[169],"eliminates":[172],"need":[174],"for":[175],"conformational":[176],"search":[177],"sampling,":[179],"it":[180],"significantly":[181],"reduces":[182],"computational":[183],"time":[184],"compared":[185],"existing":[187],"methods.":[189]},"counts_by_year":[],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}