{"id":"https://openalex.org/W4390563867","doi":"https://doi.org/10.1093/bib/bbad488","title":"Protein\u2013DNA binding sites prediction based on pre-trained protein language model and contrastive learning","display_name":"Protein\u2013DNA binding sites prediction based on pre-trained protein language model and contrastive learning","publication_year":2023,"publication_date":"2023-11-22","ids":{"openalex":"https://openalex.org/W4390563867","doi":"https://doi.org/10.1093/bib/bbad488","pmid":"https://pubmed.ncbi.nlm.nih.gov/38171929"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad488","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad488","pdf_url":"https://academic.oup.com/bib/article-pdf/25/1/bbad488/54943739/bbad488.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bib/article-pdf/25/1/bbad488/54943739/bbad488.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101868152","display_name":"Yufan Liu","orcid":"https://orcid.org/0009-0007-8781-0282"},"institutions":[{"id":"https://openalex.org/I4210098034","display_name":"Key Laboratory of Guangdong Province","ror":"https://ror.org/00swtqp09","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210098034"]},{"id":"https://openalex.org/I4391767655","display_name":"State Key Laboratory of Molecular Oncology","ror":"https://ror.org/014gmtw23","country_code":null,"type":"facility","lineage":["https://openalex.org/I4210141458","https://openalex.org/I4391767655"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yufan Liu","raw_affiliation_strings":["MOE Key Laboratory of Bioinformatics , State Key Laboratory of Molecular Oncology, School of Pharmaceutical Sciences, , Beijing, 100084 , China","Tsinghua University , State Key Laboratory of Molecular Oncology, School of Pharmaceutical Sciences, , Beijing, 100084 , China","MOE Key Laboratory of Bioinformatics, State Key Laboratory of Molecular Oncology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics , State Key Laboratory of Molecular Oncology, School of Pharmaceutical Sciences, , Beijing, 100084 , China","institution_ids":["https://openalex.org/I4210098034"]},{"raw_affiliation_string":"Tsinghua University , State Key Laboratory of Molecular Oncology, School of Pharmaceutical Sciences, , Beijing, 100084 , China","institution_ids":["https://openalex.org/I99065089","https://openalex.org/I4391767655"]},{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics, State Key Laboratory of Molecular Oncology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China","institution_ids":["https://openalex.org/I99065089","https://openalex.org/I4391767655"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5037870231","display_name":"Boxue Tian","orcid":"https://orcid.org/0000-0002-5830-0669"},"institutions":[{"id":"https://openalex.org/I4210098034","display_name":"Key Laboratory of Guangdong Province","ror":"https://ror.org/00swtqp09","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210098034"]},{"id":"https://openalex.org/I4391767655","display_name":"State Key Laboratory of Molecular Oncology","ror":"https://ror.org/014gmtw23","country_code":null,"type":"facility","lineage":["https://openalex.org/I4210141458","https://openalex.org/I4391767655"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Boxue Tian","raw_affiliation_strings":["MOE Key Laboratory of Bioinformatics , State Key Laboratory of Molecular Oncology, School of Pharmaceutical Sciences, , Beijing, 100084 , China","Tsinghua University , State Key Laboratory of Molecular Oncology, School of Pharmaceutical Sciences, , Beijing, 100084 , China","MOE Key Laboratory of Bioinformatics, State Key Laboratory of Molecular Oncology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China"],"raw_orcid":"https://orcid.org/0000-0002-5830-0669","affiliations":[{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics , State Key Laboratory of Molecular Oncology, School of Pharmaceutical Sciences, , Beijing, 100084 , China","institution_ids":["https://openalex.org/I4210098034"]},{"raw_affiliation_string":"Tsinghua University , State Key Laboratory of Molecular Oncology, School of Pharmaceutical Sciences, , Beijing, 100084 , China","institution_ids":["https://openalex.org/I99065089","https://openalex.org/I4391767655"]},{"raw_affiliation_string":"MOE Key Laboratory of Bioinformatics, State Key Laboratory of Molecular Oncology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China","institution_ids":["https://openalex.org/I99065089","https://openalex.org/I4391767655"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5101868152"],"corresponding_institution_ids":["https://openalex.org/I4210098034","https://openalex.org/I4391767655","https://openalex.org/I99065089"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":10.796,"has_fulltext":true,"cited_by_count":72,"citation_normalized_percentile":{"value":0.9888382,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"25","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9997000098228455,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9997000098228455,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9952999949455261,"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":0.6712405681610107},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.6393880248069763},{"id":"https://openalex.org/keywords/generalization","display_name":"Generalization","score":0.5989645719528198},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4891717731952667},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4569360315799713},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.36193016171455383},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16452497243881226},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.11172887682914734}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6712405681610107},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.6393880248069763},{"id":"https://openalex.org/C177148314","wikidata":"https://www.wikidata.org/wiki/Q170084","display_name":"Generalization","level":2,"score":0.5989645719528198},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4891717731952667},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4569360315799713},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.36193016171455383},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16452497243881226},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.11172887682914734},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0}],"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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007858","descriptor_name":"Learning","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":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbad488","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad488","pdf_url":"https://academic.oup.com/bib/article-pdf/25/1/bbad488/54943739/bbad488.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38171929","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38171929","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:pubmedcentral.nih.gov:10782905","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10782905","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10782905/pdf/bbad488.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":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbad488","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad488","pdf_url":"https://academic.oup.com/bib/article-pdf/25/1/bbad488/54943739/bbad488.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6193454956","display_name":null,"funder_award_id":"61020100120","funder_id":"https://openalex.org/F4320322392","funder_display_name":"Tsinghua University"},{"id":"https://openalex.org/G6781826246","display_name":null,"funder_award_id":"61020100120","funder_id":"https://openalex.org/F4320324787","funder_display_name":"Peking University"}],"funders":[{"id":"https://openalex.org/F4320322392","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549"},{"id":"https://openalex.org/F4320324787","display_name":"Peking University","ror":"https://ror.org/02v51f717"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4390563867.pdf"},"referenced_works_count":52,"referenced_works":["https://openalex.org/W1971894358","https://openalex.org/W2010541165","https://openalex.org/W2013146483","https://openalex.org/W2016160555","https://openalex.org/W2018661561","https://openalex.org/W2051210555","https://openalex.org/W2082628285","https://openalex.org/W2085836956","https://openalex.org/W2092988184","https://openalex.org/W2110505462","https://openalex.org/W2115547583","https://openalex.org/W2119948329","https://openalex.org/W2126103104","https://openalex.org/W2138977668","https://openalex.org/W2142529984","https://openalex.org/W2148143831","https://openalex.org/W2154447604","https://openalex.org/W2155393000","https://openalex.org/W2155844132","https://openalex.org/W2156125289","https://openalex.org/W2304455477","https://openalex.org/W2587935821","https://openalex.org/W2785792383","https://openalex.org/W2884055093","https://openalex.org/W2884561390","https://openalex.org/W2892720054","https://openalex.org/W2913846066","https://openalex.org/W2980282514","https://openalex.org/W3009202743","https://openalex.org/W3049692992","https://openalex.org/W3126876258","https://openalex.org/W3164365007","https://openalex.org/W3177500196","https://openalex.org/W3184675023","https://openalex.org/W3198659451","https://openalex.org/W4205989901","https://openalex.org/W4255556797","https://openalex.org/W4281294164","https://openalex.org/W4281557145","https://openalex.org/W4283011532","https://openalex.org/W4296151531","https://openalex.org/W4296472808","https://openalex.org/W4308268814","https://openalex.org/W4311456810","https://openalex.org/W4327550249","https://openalex.org/W4379932151","https://openalex.org/W4385237444","https://openalex.org/W4392302569","https://openalex.org/W6768817161","https://openalex.org/W6838508969","https://openalex.org/W6842861464","https://openalex.org/W6846409395"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W4387369504","https://openalex.org/W3046775127","https://openalex.org/W4394896187","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W3107602296","https://openalex.org/W4364306694","https://openalex.org/W4312192474"],"abstract_inverted_index":{"Protein-DNA":[0],"interaction":[1,22],"is":[2,17,165],"critical":[3],"for":[4,19,33,169],"life":[5],"activities":[6],"such":[7],"as":[8],"replication,":[9],"transcription":[10],"and":[11,23,29,51,76,97,102,129,145,181],"splicing.":[12],"Identifying":[13],"protein-DNA":[14,93],"binding":[15,84,94,159,170],"residues":[16],"essential":[18],"modeling":[20],"their":[21],"downstream":[24],"studies.":[25],"However,":[26],"developing":[27],"accurate":[28],"efficient":[30],"computational":[31],"methods":[32],"this":[34,40,55],"task":[35],"remains":[36],"challenging.":[37],"Improvements":[38],"in":[39,49],"area":[41,113],"have":[42],"the":[43,77,88,92,99,112,119,123,175,178],"potential":[44],"to":[45,81,136,148],"drive":[46],"novel":[47,60],"applications":[48],"biotechnology":[50],"drug":[52],"design.":[53],"In":[54,151],"study,":[56],"we":[57,153],"propose":[58],"a":[59,71,166],"approach":[61],"called":[62],"Contrastive":[63],"Learning":[64],"And":[65],"Pre-trained":[66],"Encoder":[67],"(CLAPE),":[68],"which":[69],"combines":[70],"pre-trained":[72],"protein":[73],"language":[74],"model":[75,90,100,121],"contrastive":[78],"learning":[79],"method":[80],"predict":[82],"DNA":[83],"residues.":[85],"We":[86],"trained":[87,154],"CLAPE-DB":[89,120,140],"on":[91,122,156],"sites":[95,160,171],"dataset":[96],"evaluated":[98],"performance":[101,134],"generalization":[103,143],"ability":[104,144],"through":[105],"various":[106],"experiments.":[107],"The":[108],"results":[109],"showed":[110,141],"that":[111,163],"under":[114],"ROC":[115],"curve":[116],"values":[117],"of":[118],"two":[124],"benchmark":[125,179],"datasets":[126,180],"reached":[127],"0.871":[128],"0.881,":[130],"respectively,":[131],"indicating":[132],"superior":[133],"compared":[135],"other":[137],"existing":[138],"models.":[139],"better":[142],"was":[146],"specific":[147],"DNA-binding":[149],"sites.":[150],"addition,":[152],"CLAPE":[155,164],"different":[157],"protein-ligand":[158],"datasets,":[161],"demonstrating":[162],"general":[167],"framework":[168],"prediction.":[172],"To":[173],"facilitate":[174],"scientific":[176],"community,":[177],"codes":[182],"are":[183],"freely":[184],"available":[185],"at":[186],"https://github.com/YAndrewL/clape.":[187]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":50},{"year":2024,"cited_by_count":18},{"year":2023,"cited_by_count":1}],"updated_date":"2026-01-20T17:24:06.736184","created_date":"2025-10-10T00:00:00"}
