{"id":"https://openalex.org/W4291143390","doi":"https://doi.org/10.1093/bib/bbac330","title":"Studying protein\u2013protein interaction through side-chain modeling method OPUS-Mut","display_name":"Studying protein\u2013protein interaction through side-chain modeling method OPUS-Mut","publication_year":2022,"publication_date":"2022-08-12","ids":{"openalex":"https://openalex.org/W4291143390","doi":"https://doi.org/10.1093/bib/bbac330","pmid":"https://pubmed.ncbi.nlm.nih.gov/35959990"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac330","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac330","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","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/A5049642190","display_name":"Gang Xu","orcid":"https://orcid.org/0000-0003-0616-878X"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4391012619","display_name":"Shanghai Artificial Intelligence Laboratory","ror":"https://ror.org/03wkvpx79","country_code":null,"type":"facility","lineage":["https://openalex.org/I4391012619"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Gang Xu","raw_affiliation_strings":["Multiscale Research Institute of Complex Systems, Fudan University , Shanghai 200433 , China","Shanghai AI Laboratory , Shanghai 200030 , China","Zhangjiang Fudan International Innovation Center, Fudan University , Shanghai 201210 , China"],"affiliations":[{"raw_affiliation_string":"Multiscale Research Institute of Complex Systems, Fudan University , Shanghai 200433 , China","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"Shanghai AI Laboratory , Shanghai 200030 , China","institution_ids":["https://openalex.org/I4391012619"]},{"raw_affiliation_string":"Zhangjiang Fudan International Innovation Center, Fudan University , Shanghai 201210 , China","institution_ids":["https://openalex.org/I24943067"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100449840","display_name":"Yilin Wang","orcid":"https://orcid.org/0000-0001-5320-0274"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yilin Wang","raw_affiliation_strings":["Georgetown Preparatory School , North Bethesda, MD 20852 , USA"],"affiliations":[{"raw_affiliation_string":"Georgetown Preparatory School , North Bethesda, MD 20852 , USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100432286","display_name":"Qinghua Wang","orcid":"https://orcid.org/0000-0001-8494-8824"},"institutions":[{"id":"https://openalex.org/I2802974365","display_name":"Shanghai Innovative Research Center of Traditional Chinese Medicine","ror":"https://ror.org/01gnagj68","country_code":"CN","type":"facility","lineage":["https://openalex.org/I2802974365"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qinghua Wang","raw_affiliation_strings":["Center for Biomolecular Innovation, Harcam Biomedicines , Shanghai , China"],"affiliations":[{"raw_affiliation_string":"Center for Biomolecular Innovation, Harcam Biomedicines , Shanghai , China","institution_ids":["https://openalex.org/I2802974365"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076174923","display_name":"Jianpeng Ma","orcid":"https://orcid.org/0000-0003-2943-0779"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4391012619","display_name":"Shanghai Artificial Intelligence Laboratory","ror":"https://ror.org/03wkvpx79","country_code":null,"type":"facility","lineage":["https://openalex.org/I4391012619"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jianpeng Ma","raw_affiliation_strings":["Multiscale Research Institute of Complex Systems, Fudan University , Shanghai 200433 , China","Shanghai AI Laboratory , Shanghai 200030 , China","Zhangjiang Fudan International Innovation Center, Fudan University , Shanghai 201210 , China"],"affiliations":[{"raw_affiliation_string":"Multiscale Research Institute of Complex Systems, Fudan University , Shanghai 200433 , China","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"Shanghai AI Laboratory , Shanghai 200030 , China","institution_ids":["https://openalex.org/I4391012619"]},{"raw_affiliation_string":"Zhangjiang Fudan International Innovation Center, Fudan University , Shanghai 201210 , China","institution_ids":["https://openalex.org/I24943067"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5076174923"],"corresponding_institution_ids":["https://openalex.org/I24943067","https://openalex.org/I4391012619"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.6065,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.64291504,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"23","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9995999932289124,"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":0.9995999932289124,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/T11162","display_name":"Enzyme Structure and Function","score":0.9904000163078308,"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/side-chain","display_name":"Side chain","score":0.8317188620567322},{"id":"https://openalex.org/keywords/dock","display_name":"DOCK","score":0.7408461570739746},{"id":"https://openalex.org/keywords/oligomer","display_name":"Oligomer","score":0.6929525136947632},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6679502129554749},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.5314915180206299},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.38495391607284546},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3598945736885071},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.35184788703918457},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.15705350041389465},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1487339735031128},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.07117071747779846}],"concepts":[{"id":"https://openalex.org/C204921945","wikidata":"https://www.wikidata.org/wiki/Q899689","display_name":"Side chain","level":3,"score":0.8317188620567322},{"id":"https://openalex.org/C93073132","wikidata":"https://www.wikidata.org/wiki/Q24726581","display_name":"DOCK","level":2,"score":0.7408461570739746},{"id":"https://openalex.org/C2780642029","wikidata":"https://www.wikidata.org/wiki/Q726004","display_name":"Oligomer","level":2,"score":0.6929525136947632},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6679502129554749},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.5314915180206299},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.38495391607284546},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3598945736885071},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.35184788703918457},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.15705350041389465},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1487339735031128},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.07117071747779846},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C521977710","wikidata":"https://www.wikidata.org/wiki/Q81163","display_name":"Polymer","level":2,"score":0.0}],"mesh":[{"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":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbac330","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac330","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35959990","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35959990","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.4699999988079071,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[{"id":"https://openalex.org/G1385649608","display_name":null,"funder_award_id":"2021YFF1200400","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"}],"funders":[{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":34,"referenced_works":["https://openalex.org/W1829437510","https://openalex.org/W1966998052","https://openalex.org/W2054394841","https://openalex.org/W2055905702","https://openalex.org/W2106648157","https://openalex.org/W2117163574","https://openalex.org/W2129454543","https://openalex.org/W2132629607","https://openalex.org/W2140943911","https://openalex.org/W2141685906","https://openalex.org/W2145778523","https://openalex.org/W2152107372","https://openalex.org/W2165371996","https://openalex.org/W2166317516","https://openalex.org/W2168505829","https://openalex.org/W2508425869","https://openalex.org/W2588962857","https://openalex.org/W2770647690","https://openalex.org/W2777503661","https://openalex.org/W2946457131","https://openalex.org/W2950365860","https://openalex.org/W2967586821","https://openalex.org/W2990458240","https://openalex.org/W2990689232","https://openalex.org/W3014576393","https://openalex.org/W3100075733","https://openalex.org/W3113626021","https://openalex.org/W3161720145","https://openalex.org/W3212562354","https://openalex.org/W4220891150","https://openalex.org/W4220933043","https://openalex.org/W4291291941","https://openalex.org/W6787662154","https://openalex.org/W6799013165"],"related_works":["https://openalex.org/W4282913408","https://openalex.org/W2100436540","https://openalex.org/W2300502530","https://openalex.org/W3201417569","https://openalex.org/W2070163817","https://openalex.org/W2395175315","https://openalex.org/W1938743025","https://openalex.org/W2102475066","https://openalex.org/W3193731429","https://openalex.org/W2050992060"],"abstract_inverted_index":{"Protein":[0],"side":[1,130],"chains":[2,131],"are":[3],"vitally":[4],"important":[5],"to":[6],"many":[7],"biological":[8],"processes":[9],"such":[10],"as":[11,94],"protein-protein":[12,69,142],"interaction.":[13,143],"In":[14],"this":[15],"study,":[16],"we":[17],"evaluate":[18],"the":[19,59,79,91,95,113,121,127],"performance":[20],"of":[21,100,129],"our":[22,65,108],"previous":[23],"released":[24],"side-chain":[25,115],"modeling":[26],"method":[27,66,109],"OPUS-Mut,":[28],"together":[29],"with":[30,120],"some":[31],"other":[32,51],"methods,":[33],"on":[34,67,72,112],"three":[35],"oligomer":[36],"datasets,":[37],"CASP14":[38],"(11),":[39],"CAMEO-Homo":[40],"(65)":[41],"and":[42,132,136],"CAMEO-Hetero":[43],"(21).":[44],"The":[45],"results":[46],"show":[47],"that":[48],"OPUS-Mut":[49],"outperforms":[50],"methods":[52],"measured":[53],"by":[54,58],"all":[55],"residues":[56],"or":[57],"interfacial":[60],"residues.":[61],"We":[62],"also":[63],"demonstrate":[64],"evaluating":[68],"docking":[70],"pose":[71,93],"a":[73,134],"dataset":[74],"Oligomer-Dock":[75],"(75)":[76],"created":[77],"using":[78],"top":[80],"10":[81],"predictions":[82],"from":[83,104],"ZDOCK":[84],"3.0.2.":[85],"Our":[86],"scoring":[87,106,138],"function":[88],"correctly":[89],"identifies":[90],"native":[92],"top-1":[96],"in":[97,118],"45":[98],"out":[99],"75":[101],"targets.":[102],"Different":[103],"traditional":[105],"functions,":[107],"is":[110],"based":[111],"overall":[114],"packing":[116,123],"favorableness":[117],"accordance":[119],"local":[122],"environment.":[124],"It":[125],"emphasizes":[126],"significance":[128],"provides":[133],"new":[135],"effective":[137],"term":[139],"for":[140],"studying":[141]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
