{"id":"https://openalex.org/W4296472808","doi":"https://doi.org/10.1093/bib/bbac322","title":"A deep learning-based method for the prediction of DNA interacting residues in a protein","display_name":"A deep learning-based method for the prediction of DNA interacting residues in a protein","publication_year":2022,"publication_date":"2022-08-08","ids":{"openalex":"https://openalex.org/W4296472808","doi":"https://doi.org/10.1093/bib/bbac322","pmid":"https://pubmed.ncbi.nlm.nih.gov/35943134"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac322","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac322","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/A5048158238","display_name":"Sumeet Patiyal","orcid":"https://orcid.org/0000-0003-1358-292X"},"institutions":[{"id":"https://openalex.org/I119939252","display_name":"Indraprastha Institute of Information Technology Delhi","ror":"https://ror.org/03vfp4g33","country_code":"IN","type":"education","lineage":["https://openalex.org/I119939252"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Sumeet Patiyal","raw_affiliation_strings":["Department of Computational Biology, Indraprastha Institute of Information Technology , Okhla Phase 3, New Delhi-110020, India"],"affiliations":[{"raw_affiliation_string":"Department of Computational Biology, Indraprastha Institute of Information Technology , Okhla Phase 3, New Delhi-110020, India","institution_ids":["https://openalex.org/I119939252"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054096262","display_name":"Anjali Dhall","orcid":"https://orcid.org/0000-0002-0400-2084"},"institutions":[{"id":"https://openalex.org/I119939252","display_name":"Indraprastha Institute of Information Technology Delhi","ror":"https://ror.org/03vfp4g33","country_code":"IN","type":"education","lineage":["https://openalex.org/I119939252"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Anjali Dhall","raw_affiliation_strings":["Department of Computational Biology, Indraprastha Institute of Information Technology , Okhla Phase 3, New Delhi-110020, India"],"affiliations":[{"raw_affiliation_string":"Department of Computational Biology, Indraprastha Institute of Information Technology , Okhla Phase 3, New Delhi-110020, India","institution_ids":["https://openalex.org/I119939252"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051938893","display_name":"Gajendra P. S. Raghava","orcid":"https://orcid.org/0000-0002-8902-2876"},"institutions":[{"id":"https://openalex.org/I119939252","display_name":"Indraprastha Institute of Information Technology Delhi","ror":"https://ror.org/03vfp4g33","country_code":"IN","type":"education","lineage":["https://openalex.org/I119939252"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Gajendra P S Raghava","raw_affiliation_strings":["Department of Computational Biology, Indraprastha Institute of Information Technology , Okhla Phase 3, New Delhi-110020, India"],"affiliations":[{"raw_affiliation_string":"Department of Computational Biology, Indraprastha Institute of Information Technology , Okhla Phase 3, New Delhi-110020, India","institution_ids":["https://openalex.org/I119939252"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5051938893"],"corresponding_institution_ids":["https://openalex.org/I119939252"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":4.5091,"has_fulltext":false,"cited_by_count":32,"citation_normalized_percentile":{"value":0.9536966,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"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/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"}},"topics":[{"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9987999796867371,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9980000257492065,"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/artificial-intelligence","display_name":"Artificial intelligence","score":0.6745160818099976},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6741476655006409},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.6055995225906372},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.555846095085144},{"id":"https://openalex.org/keywords/boosting","display_name":"Boosting (machine learning)","score":0.48923778533935547},{"id":"https://openalex.org/keywords/gradient-boosting","display_name":"Gradient boosting","score":0.46547481417655945},{"id":"https://openalex.org/keywords/rna-splicing","display_name":"RNA splicing","score":0.43085652589797974},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.4118536114692688},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.35301923751831055},{"id":"https://openalex.org/keywords/random-forest","display_name":"Random forest","score":0.24539977312088013},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.20039764046669006},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16356045007705688},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12085694074630737}],"concepts":[{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6745160818099976},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6741476655006409},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.6055995225906372},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.555846095085144},{"id":"https://openalex.org/C46686674","wikidata":"https://www.wikidata.org/wiki/Q466303","display_name":"Boosting (machine learning)","level":2,"score":0.48923778533935547},{"id":"https://openalex.org/C70153297","wikidata":"https://www.wikidata.org/wiki/Q5591907","display_name":"Gradient boosting","level":3,"score":0.46547481417655945},{"id":"https://openalex.org/C54458228","wikidata":"https://www.wikidata.org/wiki/Q237218","display_name":"RNA splicing","level":4,"score":0.43085652589797974},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.4118536114692688},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.35301923751831055},{"id":"https://openalex.org/C169258074","wikidata":"https://www.wikidata.org/wiki/Q245748","display_name":"Random forest","level":2,"score":0.24539977312088013},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.20039764046669006},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16356045007705688},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12085694074630737},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056510","descriptor_name":"Position-Specific Scoring Matrices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056510","descriptor_name":"Position-Specific Scoring Matrices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056510","descriptor_name":"Position-Specific Scoring Matrices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbac322","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac322","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:35943134","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35943134","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":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":75,"referenced_works":["https://openalex.org/W1491553314","https://openalex.org/W1543773936","https://openalex.org/W1971894358","https://openalex.org/W1975447903","https://openalex.org/W1977628834","https://openalex.org/W1981482769","https://openalex.org/W1994122295","https://openalex.org/W2000213161","https://openalex.org/W2019971393","https://openalex.org/W2028403985","https://openalex.org/W2029964710","https://openalex.org/W2032690714","https://openalex.org/W2033591223","https://openalex.org/W2038670706","https://openalex.org/W2080099205","https://openalex.org/W2089716128","https://openalex.org/W2096986143","https://openalex.org/W2097606916","https://openalex.org/W2099485600","https://openalex.org/W2118713799","https://openalex.org/W2119948329","https://openalex.org/W2122137509","https://openalex.org/W2125714273","https://openalex.org/W2128533758","https://openalex.org/W2128607518","https://openalex.org/W2130479394","https://openalex.org/W2140239055","https://openalex.org/W2141101695","https://openalex.org/W2141149420","https://openalex.org/W2145023212","https://openalex.org/W2145382385","https://openalex.org/W2147285856","https://openalex.org/W2149997286","https://openalex.org/W2152116196","https://openalex.org/W2156136208","https://openalex.org/W2157122545","https://openalex.org/W2158261944","https://openalex.org/W2158714788","https://openalex.org/W2166058140","https://openalex.org/W2169336373","https://openalex.org/W2198630282","https://openalex.org/W2314115072","https://openalex.org/W2399469784","https://openalex.org/W2411557417","https://openalex.org/W2531919408","https://openalex.org/W2582176104","https://openalex.org/W2743925332","https://openalex.org/W2766430481","https://openalex.org/W2772865572","https://openalex.org/W2883467144","https://openalex.org/W2892720054","https://openalex.org/W2901491192","https://openalex.org/W2908450496","https://openalex.org/W2924068395","https://openalex.org/W2933350524","https://openalex.org/W2933605448","https://openalex.org/W2981827938","https://openalex.org/W2998259324","https://openalex.org/W3009202743","https://openalex.org/W3092381885","https://openalex.org/W3101256226","https://openalex.org/W3104537585","https://openalex.org/W3121281384","https://openalex.org/W3126876258","https://openalex.org/W3177828909","https://openalex.org/W4205989901","https://openalex.org/W4206739112","https://openalex.org/W4213149192","https://openalex.org/W4292907187","https://openalex.org/W6680867393","https://openalex.org/W6732748968","https://openalex.org/W6749029207","https://openalex.org/W6761383852","https://openalex.org/W6785744313","https://openalex.org/W6788666452"],"related_works":["https://openalex.org/W2967733078","https://openalex.org/W3204430031","https://openalex.org/W3137904399","https://openalex.org/W4310492845","https://openalex.org/W2885778889","https://openalex.org/W4310224730","https://openalex.org/W2766514146","https://openalex.org/W4289703016","https://openalex.org/W2885516856","https://openalex.org/W3094138326"],"abstract_inverted_index":{"DNA-protein":[0],"interaction":[1],"is":[2],"one":[3],"of":[4,17,26,39,62,84,96,122,141,157,166,174],"the":[5,10,15,77,90,120,135,144,154,160,172,178,189],"most":[6],"crucial":[7],"interactions":[8],"in":[9,76,89],"biological":[11],"system,":[12],"which":[13,205],"decides":[14],"fate":[16],"many":[18],"processes":[19],"such":[20],"as":[21],"transcription,":[22],"regulation":[23],"and":[24,48,70,100,113,181,202],"splicing":[25],"genes.":[27],"In":[28,119,192],"this":[29],"study,":[30],"we":[31,198],"trained":[32,54],"our":[33,184],"models":[34,55,105],"on":[35,58,143,159,177],"a":[36,131,164],"training":[37,91],"dataset":[38,61,79,146,162,180],"646":[40],"DNA-binding":[41,64],"proteins":[42,65,75,88],"having":[43,66],"15":[44],"636":[45],"DNA":[46,68],"interacting":[47,69],"298":[49],"503":[50],"non-interacting":[51,72],"residues.":[52,73],"Our":[53],"were":[56],"evaluated":[57,171],"an":[59],"independent":[60,78,145,161,179],"46":[63],"965":[67],"9911":[71],"All":[74],"have":[80,106],"less":[81],"than":[82],"30%":[83],"sequence":[85],"similarity":[86],"with":[87],"dataset.":[92],"A":[93],"wide":[94],"range":[95],"traditional":[97],"machine":[98,123],"learning":[99,102,124],"deep":[101],"(1D-CNN)":[103],"techniques-based":[104],"been":[107],"developed":[108,199],"using":[109,147,163],"binary,":[110],"physicochemical":[111],"properties":[112],"Position-Specific":[114],"Scoring":[115],"Matrix":[116],"(PSSM)/evolutionary":[117],"profiles.":[118,169],"case":[121],"technique,":[125],"eXtreme":[126],"Gradient":[127],"Boosting-based":[128],"model":[129,152],"achieved":[130,153],"maximum":[132],"area":[133],"under":[134],"receiver":[136],"operating":[137],"characteristics":[138],"(AUROC)":[139],"curve":[140],"0.77":[142],"PSSM":[148],"profile.":[149],"Deep":[150],"learning-based":[151],"highest":[155],"AUROC":[156],"0.79":[158],"combination":[165],"all":[167,188],"three":[168],"We":[170],"performance":[173],"existing":[175,190],"methods":[176],"observed":[182],"that":[183],"proposed":[185],"method":[186],"outperformed":[187],"methods.":[191],"order":[193],"to":[194],"facilitate":[195],"scientific":[196],"community,":[197],"standalone":[200],"software":[201],"web":[203],"server,":[204],"are":[206],"accessible":[207],"from":[208],"https://webs.iiitd.edu.in/raghava/dbpred.":[209]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":13},{"year":2024,"cited_by_count":12},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":1}],"updated_date":"2026-03-26T15:22:09.906841","created_date":"2025-10-10T00:00:00"}
