{"id":"https://openalex.org/W4205989901","doi":"https://doi.org/10.1093/bib/bbab564","title":"AlphaFold2-aware protein\u2013DNA binding site prediction using graph transformer","display_name":"AlphaFold2-aware protein\u2013DNA binding site prediction using graph transformer","publication_year":2021,"publication_date":"2021-12-10","ids":{"openalex":"https://openalex.org/W4205989901","doi":"https://doi.org/10.1093/bib/bbab564","pmid":"https://pubmed.ncbi.nlm.nih.gov/35039821"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbab564","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbab564","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/A5079232368","display_name":"Qianmu Yuan","orcid":"https://orcid.org/0000-0001-6098-9103"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qianmu Yuan","raw_affiliation_strings":["School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou 510000, China"],"raw_orcid":"https://orcid.org/0000-0001-6098-9103","affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou 510000, China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100771619","display_name":"Sheng Chen","orcid":"https://orcid.org/0000-0001-7764-7097"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Sheng Chen","raw_affiliation_strings":["School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou 510000, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou 510000, China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015329746","display_name":"Jiahua Rao","orcid":"https://orcid.org/0000-0002-6840-8198"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiahua Rao","raw_affiliation_strings":["School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou 510000, China"],"raw_orcid":"https://orcid.org/0000-0002-6840-8198","affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou 510000, China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075817762","display_name":"Shuangjia Zheng","orcid":"https://orcid.org/0000-0001-9747-4285"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shuangjia Zheng","raw_affiliation_strings":["School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou 510000, China"],"raw_orcid":"https://orcid.org/0000-0001-9747-4285","affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou 510000, China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076568855","display_name":"Huiying Zhao","orcid":"https://orcid.org/0000-0001-9429-3016"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]},{"id":"https://openalex.org/I4210097354","display_name":"Sun Yat-sen Memorial Hospital","ror":"https://ror.org/01px77p81","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210097354"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Huiying Zhao","raw_affiliation_strings":["Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510000, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510000, China","institution_ids":["https://openalex.org/I4210097354","https://openalex.org/I157773358"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023539493","display_name":"Yuedong Yang","orcid":"https://orcid.org/0000-0002-6782-2813"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yuedong Yang","raw_affiliation_strings":["Key Laboratory of Machine Intelligence and Advanced Computing of MOE, Sun Yat-sen University, Guangzhou 510000, China","School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou 510000, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Machine Intelligence and Advanced Computing of MOE, Sun Yat-sen University, Guangzhou 510000, China","institution_ids":["https://openalex.org/I157773358"]},{"raw_affiliation_string":"School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou 510000, China","institution_ids":["https://openalex.org/I157773358"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5023539493"],"corresponding_institution_ids":["https://openalex.org/I157773358"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":7.0013,"has_fulltext":false,"cited_by_count":130,"citation_normalized_percentile":{"value":0.98139114,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"23","issue":"2","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":0.9988999962806702,"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/T10521","display_name":"RNA and protein synthesis mechanisms","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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6576021909713745},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.496938019990921},{"id":"https://openalex.org/keywords/matthews-correlation-coefficient","display_name":"Matthews correlation coefficient","score":0.46823257207870483},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.45378419756889343},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.43530645966529846},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.41004252433776855},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3985671401023865},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.38761407136917114},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3769776523113251},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.25360238552093506},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18023303151130676},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.153076171875},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12971976399421692},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.10554030537605286}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6576021909713745},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.496938019990921},{"id":"https://openalex.org/C164085508","wikidata":"https://www.wikidata.org/wiki/Q4811327","display_name":"Matthews correlation coefficient","level":3,"score":0.46823257207870483},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.45378419756889343},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.43530645966529846},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.41004252433776855},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3985671401023865},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.38761407136917114},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3769776523113251},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.25360238552093506},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18023303151130676},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.153076171875},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12971976399421692},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.10554030537605286},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.0},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","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":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbab564","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbab564","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:35039821","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35039821","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},{"id":"pmh:oai:research-repository.griffith.edu.au:10072/416014","is_oa":false,"landing_page_url":"http://hdl.handle.net/10072/416014","pdf_url":null,"source":{"id":"https://openalex.org/S4306402548","display_name":"Griffith Research Online (Griffith University, Queensland, Australia)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I11701301","host_organization_name":"Griffith University","host_organization_lineage":["https://openalex.org/I11701301"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5108781970","display_name":null,"funder_award_id":"61772566","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5178878423","display_name":null,"funder_award_id":"2020YFB0204803","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7142395142","display_name":null,"funder_award_id":"62041209","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":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":72,"referenced_works":["https://openalex.org/W1904666106","https://openalex.org/W1966716734","https://openalex.org/W1972978214","https://openalex.org/W1973429805","https://openalex.org/W1978113501","https://openalex.org/W2005423065","https://openalex.org/W2008708467","https://openalex.org/W2011441819","https://openalex.org/W2018661561","https://openalex.org/W2019971393","https://openalex.org/W2024005354","https://openalex.org/W2027657574","https://openalex.org/W2029964710","https://openalex.org/W2046356894","https://openalex.org/W2051210555","https://openalex.org/W2076048958","https://openalex.org/W2104707079","https://openalex.org/W2108067237","https://openalex.org/W2110483430","https://openalex.org/W2122137509","https://openalex.org/W2122401542","https://openalex.org/W2130479394","https://openalex.org/W2137981491","https://openalex.org/W2158714788","https://openalex.org/W2166248605","https://openalex.org/W2169837652","https://openalex.org/W2170747616","https://openalex.org/W2187089797","https://openalex.org/W2557595285","https://openalex.org/W2582176104","https://openalex.org/W2612690371","https://openalex.org/W2615136515","https://openalex.org/W2617750324","https://openalex.org/W2739636023","https://openalex.org/W2755853637","https://openalex.org/W2767670653","https://openalex.org/W2807540482","https://openalex.org/W2892720054","https://openalex.org/W2908351833","https://openalex.org/W2933350524","https://openalex.org/W2949155276","https://openalex.org/W2949342052","https://openalex.org/W2957874522","https://openalex.org/W2972411752","https://openalex.org/W2982552606","https://openalex.org/W2984894304","https://openalex.org/W2994678679","https://openalex.org/W3005769002","https://openalex.org/W3028589594","https://openalex.org/W3039317077","https://openalex.org/W3121082297","https://openalex.org/W3121281384","https://openalex.org/W3126876258","https://openalex.org/W3129073614","https://openalex.org/W3129125493","https://openalex.org/W3177828909","https://openalex.org/W3183967699","https://openalex.org/W3190020173","https://openalex.org/W3196030482","https://openalex.org/W3197696221","https://openalex.org/W3207643490","https://openalex.org/W3211394146","https://openalex.org/W4252684946","https://openalex.org/W4295312788","https://openalex.org/W6732748968","https://openalex.org/W6755207826","https://openalex.org/W6765474767","https://openalex.org/W6766978945","https://openalex.org/W6769989246","https://openalex.org/W6788666452","https://openalex.org/W6798407072","https://openalex.org/W6804049574"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4224009465","https://openalex.org/W4306674287","https://openalex.org/W4286629047","https://openalex.org/W4205958290","https://openalex.org/W4384212932","https://openalex.org/W4390590544","https://openalex.org/W2096195258","https://openalex.org/W2990460313","https://openalex.org/W2887039457"],"abstract_inverted_index":{"Protein-DNA":[0],"interactions":[1],"play":[2],"crucial":[3],"roles":[4],"in":[5,73,165,173],"the":[6,15,58,70,91,100,119,137,149,159,168,180,182,186,191],"biological":[7,23],"systems,":[8],"and":[9,28,30,111,130,140,171,185],"identifying":[10,86],"protein-DNA":[11],"binding":[12,101],"sites":[13],"is":[14,145,202],"first":[16],"step":[17],"for":[18,85],"mechanistic":[19],"understanding":[20],"of":[21,57,153,194],"various":[22],"activities":[24],"(such":[25],"as":[26],"transcription":[27],"repair)":[29],"designing":[31],"novel":[32],"drugs.":[33],"How":[34],"to":[35,64,117],"accurately":[36],"identify":[37],"DNA-binding":[38,87],"residues":[39,88],"from":[40],"only":[41,53],"protein":[42,74,120,128],"sequence":[43],"remains":[44],"a":[45,106,113],"challenging":[46],"task.":[47],"Currently,":[48],"most":[49],"existing":[50],"sequence-based":[51,139],"methods":[52],"consider":[54],"contextual":[55],"features":[56],"sequential":[59],"neighbors,":[60],"which":[61],"are":[62],"limited":[63],"capture":[65],"spatial":[66],"information.":[67],"Based":[68],"on":[69,90,148],"recent":[71],"breakthrough":[72],"structure":[75],"prediction":[76,103],"by":[77,95,163],"AlphaFold2,":[78],"we":[79,98],"propose":[80],"an":[81],"accurate":[82],"predictor,":[83],"GraphSite,":[84],"based":[89],"structural":[92,121],"models":[93,193],"predicted":[94,127,183],"AlphaFold2.":[96],"Here,":[97],"convert":[99],"site":[102],"problem":[104],"into":[105,123],"graph":[107,131],"node":[108],"classification":[109],"task":[110],"employ":[112],"transformer-based":[114],"variant":[115],"model":[116],"take":[118],"information":[122],"account.":[124],"By":[125],"leveraging":[126],"structures":[129,184],"transformer,":[132],"GraphSite":[133,157,195,199],"substantially":[134],"improves":[135],"over":[136],"latest":[138],"structure-based":[141,161],"methods.":[142],"The":[143,198],"algorithm":[144],"further":[146],"confirmed":[147],"independent":[150],"test":[151],"set":[152],"181":[154],"proteins,":[155],"where":[156],"surpasses":[158],"state-of-the-art":[160],"method":[162],"16.4%":[164],"area":[166],"under":[167],"precision-recall":[169],"curve":[170],"11.2%":[172],"Matthews":[174],"correlation":[175],"coefficient,":[176],"respectively.":[177],"We":[178],"provide":[179],"datasets,":[181],"source":[187],"codes":[188],"along":[189],"with":[190],"pre-trained":[192],"at":[196,205],"https://github.com/biomed-AI/GraphSite.":[197],"web":[200],"server":[201],"freely":[203],"available":[204],"https://biomed.nscc-gz.cn/apps/GraphSite.":[206]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":38},{"year":2024,"cited_by_count":49},{"year":2023,"cited_by_count":26},{"year":2022,"cited_by_count":11}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}