{"id":"https://openalex.org/W4407111218","doi":"https://doi.org/10.3389/fbinf.2025.1520382","title":"Machine learning approaches for predicting protein-ligand binding sites from sequence data","display_name":"Machine learning approaches for predicting protein-ligand binding sites from sequence data","publication_year":2025,"publication_date":"2025-02-03","ids":{"openalex":"https://openalex.org/W4407111218","doi":"https://doi.org/10.3389/fbinf.2025.1520382","pmid":"https://pubmed.ncbi.nlm.nih.gov/39963299"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2025.1520382","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1520382","pdf_url":"https://public-pages-files-2025.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1520382/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://public-pages-files-2025.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1520382/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5114553843","display_name":"Orhun Vural","orcid":"https://orcid.org/0009-0004-7918-5307"},"institutions":[{"id":"https://openalex.org/I32389192","display_name":"University of Alabama at Birmingham","ror":"https://ror.org/008s83205","country_code":"US","type":"education","lineage":["https://openalex.org/I32389192"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Orhun Vural","raw_affiliation_strings":["Department of Electrical and Computer Engineering, The University of Alabama at Birmingham, Birmingham, AL, United States"],"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, The University of Alabama at Birmingham, Birmingham, AL, United States","institution_ids":["https://openalex.org/I32389192"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5001127263","display_name":"Leon Jololian","orcid":null},"institutions":[{"id":"https://openalex.org/I32389192","display_name":"University of Alabama at Birmingham","ror":"https://ror.org/008s83205","country_code":"US","type":"education","lineage":["https://openalex.org/I32389192"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Leon Jololian","raw_affiliation_strings":["Department of Electrical and Computer Engineering, The University of Alabama at Birmingham, Birmingham, AL, United States"],"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, The University of Alabama at Birmingham, Birmingham, AL, United States","institution_ids":["https://openalex.org/I32389192"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5114553843"],"corresponding_institution_ids":["https://openalex.org/I32389192"],"apc_list":{"value":1900,"currency":"USD","value_usd":1900},"apc_paid":{"value":1900,"currency":"USD","value_usd":1900},"fwci":8.0879,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.97299225,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"5","issue":null,"first_page":"1520382","last_page":"1520382"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":1.0,"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":1.0,"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":0.9966999888420105,"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":0.9944000244140625,"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/computational-biology","display_name":"Computational biology","score":0.5826640129089355},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.573222815990448},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5314005613327026},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5216844081878662},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.5148662328720093},{"id":"https://openalex.org/keywords/protein-ligand","display_name":"Protein ligand","score":0.5123313665390015},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5049245953559875},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.47472915053367615},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.4287455677986145},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.42749589681625366},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3267938792705536},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3210054636001587},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.28661754727363586},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.13496625423431396},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.08931025862693787}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5826640129089355},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.573222815990448},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5314005613327026},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5216844081878662},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.5148662328720093},{"id":"https://openalex.org/C109095088","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Protein ligand","level":2,"score":0.5123313665390015},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5049245953559875},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.47472915053367615},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.4287455677986145},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.42749589681625366},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3267938792705536},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3210054636001587},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.28661754727363586},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.13496625423431396},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.08931025862693787},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3389/fbinf.2025.1520382","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1520382","pdf_url":"https://public-pages-files-2025.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1520382/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39963299","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39963299","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":"Frontiers in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11830693","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11830693","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11830693/pdf/fbinf-05-1520382.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":"Front Bioinform","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:d16db4f041a84ef39175fbc34bfd20e4","is_oa":true,"landing_page_url":"https://doaj.org/article/d16db4f041a84ef39175fbc34bfd20e4","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Frontiers in Bioinformatics, Vol 5 (2025)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2025.1520382","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1520382","pdf_url":"https://public-pages-files-2025.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1520382/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.4399999976158142,"id":"https://metadata.un.org/sdg/3"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4407111218.pdf","grobid_xml":"https://content.openalex.org/works/W4407111218.grobid-xml"},"referenced_works_count":96,"referenced_works":["https://openalex.org/W24553703","https://openalex.org/W255996521","https://openalex.org/W1501531009","https://openalex.org/W1538131130","https://openalex.org/W1614298861","https://openalex.org/W1964880253","https://openalex.org/W1980969309","https://openalex.org/W2004377868","https://openalex.org/W2043338013","https://openalex.org/W2051210555","https://openalex.org/W2064675550","https://openalex.org/W2071557543","https://openalex.org/W2076048958","https://openalex.org/W2076052898","https://openalex.org/W2096495474","https://openalex.org/W2107024517","https://openalex.org/W2113985551","https://openalex.org/W2114162221","https://openalex.org/W2116341502","https://openalex.org/W2123622386","https://openalex.org/W2131617076","https://openalex.org/W2131774270","https://openalex.org/W2136799255","https://openalex.org/W2140538197","https://openalex.org/W2147526198","https://openalex.org/W2194775991","https://openalex.org/W2343614482","https://openalex.org/W2739999456","https://openalex.org/W2887981960","https://openalex.org/W2903705089","https://openalex.org/W2918335507","https://openalex.org/W2940438782","https://openalex.org/W2955690154","https://openalex.org/W2964015378","https://openalex.org/W2964019776","https://openalex.org/W2973993756","https://openalex.org/W2980789587","https://openalex.org/W2987090428","https://openalex.org/W2995514860","https://openalex.org/W2999309192","https://openalex.org/W3006477052","https://openalex.org/W3007077815","https://openalex.org/W3007743886","https://openalex.org/W3008730383","https://openalex.org/W3012511738","https://openalex.org/W3080555959","https://openalex.org/W3129471271","https://openalex.org/W3132200718","https://openalex.org/W3146944767","https://openalex.org/W3153418506","https://openalex.org/W3157853087","https://openalex.org/W3165603781","https://openalex.org/W3167479850","https://openalex.org/W3177500196","https://openalex.org/W3184324824","https://openalex.org/W3197542363","https://openalex.org/W3205598784","https://openalex.org/W3213922610","https://openalex.org/W4206002704","https://openalex.org/W4206940890","https://openalex.org/W4210842338","https://openalex.org/W4225775361","https://openalex.org/W4225891318","https://openalex.org/W4236358448","https://openalex.org/W4281720176","https://openalex.org/W4285081903","https://openalex.org/W4292779060","https://openalex.org/W4295088922","https://openalex.org/W4297733535","https://openalex.org/W4310057196","https://openalex.org/W4313525416","https://openalex.org/W4313527276","https://openalex.org/W4320731502","https://openalex.org/W4327550249","https://openalex.org/W4327566741","https://openalex.org/W4364351976","https://openalex.org/W4367049415","https://openalex.org/W4385245566","https://openalex.org/W4385407166","https://openalex.org/W4385838908","https://openalex.org/W4387761568","https://openalex.org/W4387859889","https://openalex.org/W4388140476","https://openalex.org/W4389470796","https://openalex.org/W4389980359","https://openalex.org/W4390793818","https://openalex.org/W4392452451","https://openalex.org/W4396721167","https://openalex.org/W4399893066","https://openalex.org/W4401745254","https://openalex.org/W4405090494","https://openalex.org/W6632100814","https://openalex.org/W6687483927","https://openalex.org/W6791955017","https://openalex.org/W6848210984","https://openalex.org/W6849401121"],"related_works":["https://openalex.org/W2480711475","https://openalex.org/W2061997414","https://openalex.org/W1587522533","https://openalex.org/W2153190755","https://openalex.org/W2355466661","https://openalex.org/W2803627340","https://openalex.org/W1485106526","https://openalex.org/W2011432577","https://openalex.org/W3008230527","https://openalex.org/W3131522312"],"abstract_inverted_index":{"Proteins,":[0],"composed":[1],"of":[2,11,20,49,81,149,163],"amino":[3],"acids,":[4],"are":[5,131,141],"crucial":[6],"for":[7,28,137,152],"a":[8,146],"wide":[9],"range":[10],"biological":[12,45],"functions.":[13,46],"Proteins":[14],"have":[15],"various":[16,107],"interaction":[17],"sites,":[18,156],"one":[19],"which":[21],"is":[22,53],"the":[23,79,118,122,128,139,160],"protein-ligand":[24,82,94,154],"binding":[25,51,95,155],"site,":[26],"essential":[27],"molecular":[29],"interactions":[30],"and":[31,64,110,117,133,165],"biochemical":[32],"reactions.":[33],"These":[34],"sites":[35,52,96],"enable":[36],"proteins":[37],"to":[38,60,74,92],"bind":[39],"with":[40],"other":[41],"molecules,":[42],"facilitating":[43],"key":[44],"Accurate":[47],"prediction":[48,80],"these":[50],"pivotal":[54],"in":[55,121,127],"computational":[56],"drug":[57],"discovery,":[58],"helping":[59],"identify":[61],"therapeutic":[62],"targets":[63],"facilitate":[65],"treatment":[66],"development.":[67],"Machine":[68],"learning":[69,91,112],"has":[70],"made":[71],"significant":[72],"contributions":[73],"this":[75],"field":[76,140],"by":[77],"improving":[78],"interactions.":[83],"This":[84,143],"paper":[85],"reviews":[86],"studies":[87],"that":[88],"use":[89],"machine":[90,111],"predict":[93],"from":[97],"sequence":[98],"data,":[99],"focusing":[100],"on":[101],"recent":[102],"advancements.":[103],"The":[104],"review":[105],"examines":[106],"embedding":[108],"methods":[109],"architectures,":[113],"addressing":[114],"current":[115,161],"challenges":[116],"ongoing":[119],"debates":[120],"field.":[123],"Additionally,":[124],"research":[125,164],"gaps":[126],"existing":[129],"literature":[130],"highlighted,":[132],"potential":[134],"future":[135,166],"directions":[136],"advancing":[138],"discussed.":[142],"study":[144],"provides":[145],"thorough":[147],"overview":[148],"sequence-based":[150],"approaches":[151],"predicting":[153],"offering":[157],"insights":[158],"into":[159],"state":[162],"possibilities.":[167]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":5}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
