{"id":"https://openalex.org/W4408726149","doi":"https://doi.org/10.1021/acs.jcim.5c00016","title":"ATP-Pred: Prediction of Protein-ATP Binding Residues via Fusion of Residue-Level Embeddings and Kolmogorov\u2013Arnold Network","display_name":"ATP-Pred: Prediction of Protein-ATP Binding Residues via Fusion of Residue-Level Embeddings and Kolmogorov\u2013Arnold Network","publication_year":2025,"publication_date":"2025-03-22","ids":{"openalex":"https://openalex.org/W4408726149","doi":"https://doi.org/10.1021/acs.jcim.5c00016","pmid":"https://pubmed.ncbi.nlm.nih.gov/40119803"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c00016","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00016","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","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/A5111348177","display_name":"Lingrong Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I44675526","display_name":"Shanghai Ocean University","ror":"https://ror.org/04n40zv07","country_code":"CN","type":"education","lineage":["https://openalex.org/I44675526"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lingrong Zhang","raw_affiliation_strings":["College of Information Technology","Shanghai Ocean University","College of Information Technology, Shanghai Ocean University, Shanghai 201306, China"],"affiliations":[{"raw_affiliation_string":"College of Information Technology","institution_ids":[]},{"raw_affiliation_string":"Shanghai Ocean University","institution_ids":["https://openalex.org/I44675526"]},{"raw_affiliation_string":"College of Information Technology, Shanghai Ocean University, Shanghai 201306, China","institution_ids":["https://openalex.org/I44675526"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5011641116","display_name":"Taigang Liu","orcid":"https://orcid.org/0000-0002-8449-9667"},"institutions":[{"id":"https://openalex.org/I44675526","display_name":"Shanghai Ocean University","ror":"https://ror.org/04n40zv07","country_code":"CN","type":"education","lineage":["https://openalex.org/I44675526"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Taigang Liu","raw_affiliation_strings":["College of Information Technology","Shanghai Ocean University","College of Information Technology, Shanghai Ocean University, Shanghai 201306, China"],"affiliations":[{"raw_affiliation_string":"College of Information Technology","institution_ids":[]},{"raw_affiliation_string":"Shanghai Ocean University","institution_ids":["https://openalex.org/I44675526"]},{"raw_affiliation_string":"College of Information Technology, Shanghai Ocean University, Shanghai 201306, China","institution_ids":["https://openalex.org/I44675526"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5011641116"],"corresponding_institution_ids":["https://openalex.org/I44675526"],"apc_list":null,"apc_paid":null,"fwci":4.0747,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.93381244,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"65","issue":"7","first_page":"3812","last_page":"3826"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9986000061035156,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9986000061035156,"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":0.9984999895095825,"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":0.9968000054359436,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/residue","display_name":"Residue (chemistry)","score":0.656528115272522},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4986259937286377},{"id":"https://openalex.org/keywords/fusion","display_name":"Fusion","score":0.45282137393951416},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.436318039894104},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.3586105704307556},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.26020586490631104},{"id":"https://openalex.org/keywords/philosophy","display_name":"Philosophy","score":0.08515062928199768}],"concepts":[{"id":"https://openalex.org/C2781338088","wikidata":"https://www.wikidata.org/wiki/Q903495","display_name":"Residue (chemistry)","level":2,"score":0.656528115272522},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4986259937286377},{"id":"https://openalex.org/C158525013","wikidata":"https://www.wikidata.org/wiki/Q2593739","display_name":"Fusion","level":2,"score":0.45282137393951416},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.436318039894104},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.3586105704307556},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.26020586490631104},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.08515062928199768},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000255","descriptor_name":"Adenosine Triphosphate","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000255","descriptor_name":"Adenosine Triphosphate","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"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":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.5c00016","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00016","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:40119803","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40119803","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":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.4399999976158142,"display_name":"Zero hunger","id":"https://metadata.un.org/sdg/2"}],"awards":[{"id":"https://openalex.org/G7659378840","display_name":null,"funder_award_id":"11601324","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":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":60,"referenced_works":["https://openalex.org/W1489326505","https://openalex.org/W1987134040","https://openalex.org/W2010468965","https://openalex.org/W2043638247","https://openalex.org/W2047544230","https://openalex.org/W2074367516","https://openalex.org/W2076189832","https://openalex.org/W2102461176","https://openalex.org/W2140538197","https://openalex.org/W2145023212","https://openalex.org/W2170747616","https://openalex.org/W2260093441","https://openalex.org/W2523197788","https://openalex.org/W2568617656","https://openalex.org/W2785269871","https://openalex.org/W2791231776","https://openalex.org/W2949342052","https://openalex.org/W3001131586","https://openalex.org/W3007077815","https://openalex.org/W3039408146","https://openalex.org/W3121324275","https://openalex.org/W3123012027","https://openalex.org/W3152441409","https://openalex.org/W3162519132","https://openalex.org/W3177500196","https://openalex.org/W3177828909","https://openalex.org/W3189787391","https://openalex.org/W3200998130","https://openalex.org/W3202848468","https://openalex.org/W3212038543","https://openalex.org/W3215225492","https://openalex.org/W4200079916","https://openalex.org/W4205773061","https://openalex.org/W4205811961","https://openalex.org/W4225438928","https://openalex.org/W4286751634","https://openalex.org/W4301374198","https://openalex.org/W4315621831","https://openalex.org/W4317651593","https://openalex.org/W4319983921","https://openalex.org/W4327550249","https://openalex.org/W4366603469","https://openalex.org/W4386347443","https://openalex.org/W4388464011","https://openalex.org/W4390046779","https://openalex.org/W4390678101","https://openalex.org/W4390740875","https://openalex.org/W4391788775","https://openalex.org/W4392368999","https://openalex.org/W4395000641","https://openalex.org/W4396572253","https://openalex.org/W4400420070","https://openalex.org/W4401030854","https://openalex.org/W4401435582","https://openalex.org/W4401966068","https://openalex.org/W4402329624","https://openalex.org/W4402596482","https://openalex.org/W4402738661","https://openalex.org/W4403006884","https://openalex.org/W4404447386"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2899084033","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W4391375266","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W1976181487"],"abstract_inverted_index":{"Accurately":[0],"identifying":[1],"protein-ATP":[2],"binding":[3,138],"residues":[4,61],"is":[5,152],"essential":[6],"for":[7,30,58],"understanding":[8],"biological":[9],"processes":[10],"and":[11,27,79,95,155],"designing":[12],"drugs.":[13],"However,":[14],"current":[15],"sequence-based":[16,56],"methods":[17,35],"have":[18],"limitations,":[19],"such":[20],"as":[21],"difficulties":[22],"in":[23,44,62],"extracting":[24],"discriminative":[25],"features":[26],"the":[28,101],"need":[29],"more":[31],"efficient":[32],"algorithms.":[33],"Additionally,":[34],"based":[36],"on":[37,117,135],"multiple":[38],"sequence":[39],"alignments":[40],"often":[41],"face":[42],"challenges":[43],"handling":[45],"large-scale":[46],"predictions.":[47],"To":[48,104],"address":[49],"these":[50],"issues,":[51],"we":[52,108],"developed":[53,73],"ATP-Pred,":[54],"a":[55,92,96,110,153],"method":[57],"predicting":[59],"ATP-binding":[60],"proteins.":[63],"This":[64],"model":[65],"applies":[66],"transfer":[67],"learning":[68],"by":[69],"using":[70],"two":[71],"recently":[72],"pretrain":[74],"protein":[75,87],"language":[76],"models,":[77],"Ankh":[78],"ProstT5,":[80],"to":[81,99],"extract":[82],"residue-level":[83],"embeddings":[84],"that":[85,124,150],"capture":[86],"functionality.":[88],"ATP-Pred":[89,125,151],"also":[90],"integrates":[91],"CNN-BiLSTM":[93],"network":[94,98],"Kolmogorov-Arnold":[97],"build":[100],"prediction":[102],"model.":[103],"handle":[105],"data":[106,121,140],"imbalance,":[107],"introduced":[109],"weighted":[111],"focal":[112],"loss":[113],"function.":[114],"Experimental":[115],"results":[116],"three":[118],"independent":[119],"test":[120],"sets":[122],"showed":[123],"outperforms":[126],"most":[127],"existing":[128],"methods.":[129],"Its":[130],"generalizability":[131],"was":[132],"further":[133],"validated":[134],"four":[136],"protein-mononucleotide":[137],"residue":[139],"sets,":[141],"where":[142],"it":[143],"delivered":[144],"promising":[145],"results.":[146],"These":[147],"findings":[148],"suggest":[149],"robust":[154],"reliable":[156],"predictor.":[157]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4}],"updated_date":"2026-03-27T14:29:43.386196","created_date":"2025-10-10T00:00:00"}
