{"id":"https://openalex.org/W4389076414","doi":"https://doi.org/10.1093/bioinformatics/btad718","title":"DeepProSite: structure-aware protein binding site prediction using ESMFold and pretrained language model","display_name":"DeepProSite: structure-aware protein binding site prediction using ESMFold and pretrained language model","publication_year":2023,"publication_date":"2023-11-28","ids":{"openalex":"https://openalex.org/W4389076414","doi":"https://doi.org/10.1093/bioinformatics/btad718","pmid":"https://pubmed.ncbi.nlm.nih.gov/38015872"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad718","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad718","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad718/53896003/btad718.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad718/53896003/btad718.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037638343","display_name":"Yitian Fang","orcid":null},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I4210136793","display_name":"Peng Cheng Laboratory","ror":"https://ror.org/03qdqbt06","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210136793"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yitian Fang","raw_affiliation_strings":["Peng Cheng Laboratory , Shenzhen 518055, China","State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Research Laboratory of Metabolic & Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , Shanghai 200040, China","Peng Cheng Laboratory, Shenzhen, Guangdong 518055, China"],"raw_orcid":"https://orcid.org/0000-0002-4644-1464","affiliations":[{"raw_affiliation_string":"Peng Cheng Laboratory , Shenzhen 518055, China","institution_ids":["https://openalex.org/I4210136793"]},{"raw_affiliation_string":"State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Research Laboratory of Metabolic & Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , Shanghai 200040, China","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"Peng Cheng Laboratory, Shenzhen, Guangdong 518055, China","institution_ids":["https://openalex.org/I4210136793"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100620236","display_name":"Yi Jiang","orcid":"https://orcid.org/0000-0002-6618-5437"},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yi Jiang","raw_affiliation_strings":["Department of Biomedical Informatics, College of Medicine, The Ohio State University , Columbus, OH 43210, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, College of Medicine, The Ohio State University , Columbus, OH 43210, USA","institution_ids":["https://openalex.org/I52357470"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033232360","display_name":"Leyi Wei","orcid":"https://orcid.org/0000-0003-1444-190X"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Leyi Wei","raw_affiliation_strings":["School of Software, Shandong University , Jinan, Shandong 250100, China"],"raw_orcid":"https://orcid.org/0000-0003-1444-190X","affiliations":[{"raw_affiliation_string":"School of Software, Shandong University , Jinan, Shandong 250100, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022408570","display_name":"Qin Ma","orcid":"https://orcid.org/0000-0002-3264-8392"},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qin Ma","raw_affiliation_strings":["Department of Biomedical Informatics, College of Medicine, The Ohio State University , Columbus, OH 43210, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, College of Medicine, The Ohio State University , Columbus, OH 43210, USA","institution_ids":["https://openalex.org/I52357470"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070028902","display_name":"Zhixiang Ren","orcid":"https://orcid.org/0000-0002-4104-3790"},"institutions":[{"id":"https://openalex.org/I4210136793","display_name":"Peng Cheng Laboratory","ror":"https://ror.org/03qdqbt06","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210136793"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhixiang Ren","raw_affiliation_strings":["Peng Cheng Laboratory , Shenzhen 518055, China","Peng Cheng Laboratory, Shenzhen, Guangdong 518055, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Peng Cheng Laboratory , Shenzhen 518055, China","institution_ids":["https://openalex.org/I4210136793"]},{"raw_affiliation_string":"Peng Cheng Laboratory, Shenzhen, Guangdong 518055, China","institution_ids":["https://openalex.org/I4210136793"]}]},{"author_position":"middle","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","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"]},{"raw_affiliation_string":"School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, 510000, China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5041491902","display_name":"Dong\u2010Qing Wei","orcid":"https://orcid.org/0000-0003-4200-7502"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I4210136793","display_name":"Peng Cheng Laboratory","ror":"https://ror.org/03qdqbt06","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210136793"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dong-Qing Wei","raw_affiliation_strings":["Peng Cheng Laboratory , Shenzhen 518055, China","State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Research Laboratory of Metabolic & Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , Shanghai 200040, China","Peng Cheng Laboratory, Shenzhen, Guangdong 518055, China"],"raw_orcid":"https://orcid.org/0000-0003-4200-7502","affiliations":[{"raw_affiliation_string":"Peng Cheng Laboratory , Shenzhen 518055, China","institution_ids":["https://openalex.org/I4210136793"]},{"raw_affiliation_string":"State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Research Laboratory of Metabolic & Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , Shanghai 200040, China","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"Peng Cheng Laboratory, Shenzhen, Guangdong 518055, China","institution_ids":["https://openalex.org/I4210136793"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":8.9152,"has_fulltext":true,"cited_by_count":95,"citation_normalized_percentile":{"value":0.98824598,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"39","issue":"12","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":0.5167999863624573,"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":0.5167999863624573,"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":0.18520000576972961,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.18330000340938568,"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":0.7122765779495239},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4565623998641968},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.4445127248764038},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.36021801829338074}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7122765779495239},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4565623998641968},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.4445127248764038},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.36021801829338074}],"mesh":[{"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":"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":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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},{"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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad718","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad718","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad718/53896003/btad718.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38015872","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38015872","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10723037","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10723037","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10723037/pdf/btad718.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad718","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad718","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad718/53896003/btad718.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.41999998688697815,"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals"}],"awards":[{"id":"https://openalex.org/G1369294023","display_name":null,"funder_award_id":"2023YFE0199200","funder_id":"https://openalex.org/F4320322999","funder_display_name":"Shanghai Jiao Tong University"},{"id":"https://openalex.org/G2191216477","display_name":null,"funder_award_id":"32030063","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3487798717","display_name":null,"funder_award_id":"YG2021ZD02","funder_id":"https://openalex.org/F4320322999","funder_display_name":"Shanghai Jiao Tong University"},{"id":"https://openalex.org/G4016822921","display_name":null,"funder_award_id":"YG2019GD01","funder_id":"https://openalex.org/F4320322999","funder_display_name":"Shanghai Jiao Tong University"},{"id":"https://openalex.org/G4043378463","display_name":null,"funder_award_id":"61832019","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5069956715","display_name":null,"funder_award_id":"YG2019ZDA12","funder_id":"https://openalex.org/F4320322999","funder_display_name":"Shanghai Jiao Tong University"},{"id":"https://openalex.org/G5473558399","display_name":null,"funder_award_id":"19430750600","funder_id":"https://openalex.org/F4320321885","funder_display_name":"Science and Technology Commission of Shanghai Municipality"},{"id":"https://openalex.org/G6132224603","display_name":null,"funder_award_id":"62172274","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6321025814","display_name":null,"funder_award_id":"ZH2018QNA41","funder_id":"https://openalex.org/F4320322999","funder_display_name":"Shanghai Jiao Tong University"},{"id":"https://openalex.org/G7473972287","display_name":null,"funder_award_id":"32070662","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8781770150","display_name":null,"funder_award_id":"2016YFA0501703","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321885","display_name":"Science and Technology Commission of Shanghai Municipality","ror":"https://ror.org/03kt66j61"},{"id":"https://openalex.org/F4320322999","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4389076414.pdf"},"referenced_works_count":82,"referenced_works":["https://openalex.org/W161796404","https://openalex.org/W1768303176","https://openalex.org/W1978113501","https://openalex.org/W1983142511","https://openalex.org/W1992450378","https://openalex.org/W1993263392","https://openalex.org/W2001457899","https://openalex.org/W2006192061","https://openalex.org/W2008708467","https://openalex.org/W2009672036","https://openalex.org/W2016959837","https://openalex.org/W2018661561","https://openalex.org/W2033726949","https://openalex.org/W2039473152","https://openalex.org/W2041000185","https://openalex.org/W2043638247","https://openalex.org/W2050000500","https://openalex.org/W2050526879","https://openalex.org/W2056169996","https://openalex.org/W2059942519","https://openalex.org/W2060772618","https://openalex.org/W2085656056","https://openalex.org/W2102461176","https://openalex.org/W2108067237","https://openalex.org/W2108134720","https://openalex.org/W2109444605","https://openalex.org/W2110483430","https://openalex.org/W2119164128","https://openalex.org/W2130479394","https://openalex.org/W2140538197","https://openalex.org/W2141627824","https://openalex.org/W2144162005","https://openalex.org/W2145080853","https://openalex.org/W2151412657","https://openalex.org/W2155194485","https://openalex.org/W2159247900","https://openalex.org/W2162220273","https://openalex.org/W2162682281","https://openalex.org/W2170835800","https://openalex.org/W2216040507","https://openalex.org/W2264362083","https://openalex.org/W2399190924","https://openalex.org/W2472103865","https://openalex.org/W2554908696","https://openalex.org/W2619370444","https://openalex.org/W2724823461","https://openalex.org/W2757108520","https://openalex.org/W2766509651","https://openalex.org/W2785269871","https://openalex.org/W2808043011","https://openalex.org/W2904243413","https://openalex.org/W2933350524","https://openalex.org/W2944679105","https://openalex.org/W2949342052","https://openalex.org/W2955690154","https://openalex.org/W2957874522","https://openalex.org/W2971405760","https://openalex.org/W2992752586","https://openalex.org/W2994678679","https://openalex.org/W3001942526","https://openalex.org/W3007077815","https://openalex.org/W3009202743","https://openalex.org/W3016691329","https://openalex.org/W3028589594","https://openalex.org/W3080498684","https://openalex.org/W3126876258","https://openalex.org/W3129073614","https://openalex.org/W3177500196","https://openalex.org/W3177828909","https://openalex.org/W3186179742","https://openalex.org/W3197696221","https://openalex.org/W3211394146","https://openalex.org/W4205989901","https://openalex.org/W4229031603","https://openalex.org/W4281294164","https://openalex.org/W4309362167","https://openalex.org/W4327550249","https://openalex.org/W4366279959","https://openalex.org/W4385245566","https://openalex.org/W6739901393","https://openalex.org/W6765474767","https://openalex.org/W6804049574"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W3046775127","https://openalex.org/W3107602296","https://openalex.org/W4394896187","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W4364306694","https://openalex.org/W4312192474","https://openalex.org/W4283697347"],"abstract_inverted_index":{"MOTIVATION:":[0],"Identifying":[1],"the":[2,10,136,164,167],"functional":[3],"sites":[4,12,140],"of":[5,13,138,159,166],"a":[6,57],"protein,":[7],"such":[8],"as":[9,38,56,96,163],"binding":[11,63,93,103,139],"proteins,":[14],"peptides,":[15],"or":[16],"other":[17,145],"biological":[18,25],"components,":[19],"is":[20,54,132,161],"crucial":[21],"for":[22,60,141,155],"understanding":[23],"related":[24],"processes":[26],"and":[27,45,69,79,91,109,144,175],"drug":[28],"design.":[29],"However,":[30],"existing":[31],"sequence-based":[32],"methods":[33,111],"have":[34],"limited":[35],"predictive":[36],"accuracy,":[37],"they":[39],"only":[40],"consider":[41],"sequence-adjacent":[42],"contextual":[43],"features":[44],"lack":[46],"structural":[47],"information.":[48,71],"RESULTS:":[49],"In":[50,100],"this":[51],"study,":[52],"DeepProSite":[53,72,105,116,131,185],"presented":[55],"new":[58],"framework":[59],"identifying":[61],"protein":[62,67,75],"site":[64,94],"that":[65],"utilizes":[66],"structure":[68],"sequence":[70,80],"first":[73],"generates":[74],"structures":[76],"from":[77,82],"ESMFold":[78],"representations":[81],"pretrained":[83],"language":[84],"models.":[85],"It":[86],"then":[87],"uses":[88],"Graph":[89],"Transformer":[90],"formulates":[92],"predictions":[95],"graph":[97],"node":[98],"classifications.":[99],"predicting":[101,121,156],"protein-protein/peptide":[102],"sites,":[104],"outperforms":[106],"state-of-the-art":[107],"sequence-":[108],"structure-based":[110,128],"on":[112],"most":[113],"metrics.":[114],"Moreover,":[115],"maintains":[117],"its":[118,148],"performance":[119],"when":[120],"unbound":[122],"structures,":[123],"in":[124],"contrast":[125],"to":[126,135],"competing":[127],"prediction":[129,137],"methods.":[130],"also":[133],"extended":[134],"nucleic":[142],"acids":[143],"ligands,":[146],"verifying":[147],"generalization":[149],"capability.":[150],"Finally,":[151],"an":[152],"online":[153],"server":[154],"multiple":[157],"types":[158],"residue":[160],"established":[162],"implementation":[165],"proposed":[168,184],"DeepProSite.":[169],"AVAILABILITY":[170],"AND":[171],"IMPLEMENTATION:":[172],"The":[173,183],"datasets":[174],"source":[176],"codes":[177],"can":[178,186],"be":[179,187],"accessed":[180,188],"at":[181,189],"https://github.com/WeiLab-Biology/DeepProSite.":[182],"https://inner.wei-group.net/DeepProSite/.":[190]},"counts_by_year":[{"year":2026,"cited_by_count":19},{"year":2025,"cited_by_count":53},{"year":2024,"cited_by_count":23}],"updated_date":"2026-07-21T08:15:58.654021","created_date":"2025-10-10T00:00:00"}
