{"id":"https://openalex.org/W7113901839","doi":"https://doi.org/10.1145/3765612.3767221","title":"Hidden in protein sequences: Predicting cryptic binding sites","display_name":"Hidden in protein sequences: Predicting cryptic binding sites","publication_year":2025,"publication_date":"2025-10-12","ids":{"openalex":"https://openalex.org/W7113901839","doi":"https://doi.org/10.1145/3765612.3767221"},"language":null,"primary_location":{"id":"doi:10.1145/3765612.3767221","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3765612.3767221","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3765612.3767221","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 16th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://dl.acm.org/doi/pdf/10.1145/3765612.3767221","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"V\u00edt \u0160krh\u00e1k","orcid":"https://orcid.org/0009-0007-0712-0661"},"institutions":[{"id":"https://openalex.org/I21250087","display_name":"Charles University","ror":"https://ror.org/024d6js02","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21250087"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"V\u00edt \u0160krh\u00e1k","raw_affiliation_strings":["Charles University, Prague, Czech Republic"],"raw_orcid":"https://orcid.org/0009-0007-0712-0661","affiliations":[{"raw_affiliation_string":"Charles University, Prague, Czech Republic","institution_ids":["https://openalex.org/I21250087"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Hamza Gamouh","orcid":"https://orcid.org/0009-0005-2584-727X"},"institutions":[{"id":"https://openalex.org/I21250087","display_name":"Charles University","ror":"https://ror.org/024d6js02","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21250087"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Hamza Gamouh","raw_affiliation_strings":["Charles University, Prague, Czech Republic"],"raw_orcid":"https://orcid.org/0009-0005-2584-727X","affiliations":[{"raw_affiliation_string":"Charles University, Prague, Czech Republic","institution_ids":["https://openalex.org/I21250087"]}]},{"author_position":"last","author":{"id":null,"display_name":"David Hoksza","orcid":"https://orcid.org/0000-0003-4679-0557"},"institutions":[{"id":"https://openalex.org/I21250087","display_name":"Charles University","ror":"https://ror.org/024d6js02","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21250087"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"David Hoksza","raw_affiliation_strings":["Charles University, Prague, Czech Republic"],"raw_orcid":"https://orcid.org/0000-0003-4679-0557","affiliations":[{"raw_affiliation_string":"Charles University, Prague, Czech Republic","institution_ids":["https://openalex.org/I21250087"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.7279,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.86193182,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.597599983215332,"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":0.597599983215332,"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":0.22020000219345093,"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":0.08299999684095383,"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/leverage","display_name":"Leverage (statistics)","score":0.8065000176429749},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.461899995803833},{"id":"https://openalex.org/keywords/baseline","display_name":"Baseline (sea)","score":0.41819998621940613},{"id":"https://openalex.org/keywords/training-set","display_name":"Training set","score":0.40709999203681946},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.3986999988555908},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.3718999922275543},{"id":"https://openalex.org/keywords/surface-protein","display_name":"Surface protein","score":0.37119999527931213}],"concepts":[{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.8065000176429749},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5673999786376953},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.507099986076355},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.48350000381469727},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.461899995803833},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.44679999351501465},{"id":"https://openalex.org/C12725497","wikidata":"https://www.wikidata.org/wiki/Q810247","display_name":"Baseline (sea)","level":2,"score":0.41819998621940613},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.40709999203681946},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.3986999988555908},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.3718999922275543},{"id":"https://openalex.org/C3019232848","wikidata":"https://www.wikidata.org/wiki/Q29548","display_name":"Surface protein","level":2,"score":0.37119999527931213},{"id":"https://openalex.org/C51639874","wikidata":"https://www.wikidata.org/wiki/Q167149","display_name":"Plasma protein binding","level":2,"score":0.35089999437332153},{"id":"https://openalex.org/C150899416","wikidata":"https://www.wikidata.org/wiki/Q1820378","display_name":"Transfer of learning","level":2,"score":0.3483999967575073},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.3474000096321106},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.3183000087738037},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3181000053882599},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.2994000017642975},{"id":"https://openalex.org/C47822265","wikidata":"https://www.wikidata.org/wiki/Q854457","display_name":"Complex system","level":2,"score":0.2809000015258789},{"id":"https://openalex.org/C2909613950","wikidata":"https://www.wikidata.org/wiki/Q158695","display_name":"Protein Interaction Networks","level":3,"score":0.26350000500679016},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.2619999945163727}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3765612.3767221","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3765612.3767221","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3765612.3767221","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 16th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/3765612.3767221","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3765612.3767221","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3765612.3767221","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 16th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1983877833","display_name":null,"funder_award_id":"90254","funder_id":"https://openalex.org/F4320321005","funder_display_name":"Ministerstvo \u0160kolstv\u00ed, Ml\u00e1de\u017ee a T\u011blov\u00fdchovy"},{"id":"https://openalex.org/G208869049","display_name":null,"funder_award_id":"ID: 90254","funder_id":"https://openalex.org/F4320321005","funder_display_name":"Ministerstvo \u0160kolstv\u00ed, Ml\u00e1de\u017ee a T\u011blov\u00fdchovy"},{"id":"https://openalex.org/G5960638817","display_name":null,"funder_award_id":"90254","funder_id":"https://openalex.org/F4320309755","funder_display_name":"Univerzita Karlova v Praze"},{"id":"https://openalex.org/G6684038118","display_name":null,"funder_award_id":"LM2018131","funder_id":"https://openalex.org/F4320309755","funder_display_name":"Univerzita Karlova v Praze"},{"id":"https://openalex.org/G7369677097","display_name":null,"funder_award_id":"23-07349S","funder_id":"https://openalex.org/F4320321006","funder_display_name":"Grantov\u00e1 Agentura \u010cesk\u00e9 Republiky"},{"id":"https://openalex.org/G8227998441","display_name":null,"funder_award_id":"90254","funder_id":"https://openalex.org/F4320321006","funder_display_name":"Grantov\u00e1 Agentura \u010cesk\u00e9 Republiky"},{"id":"https://openalex.org/G954903593","display_name":null,"funder_award_id":"LM2018131","funder_id":"https://openalex.org/F4320321005","funder_display_name":"Ministerstvo \u0160kolstv\u00ed, Ml\u00e1de\u017ee a T\u011blov\u00fdchovy"}],"funders":[{"id":"https://openalex.org/F4320309755","display_name":"Univerzita Karlova v Praze","ror":"https://ror.org/024d6js02"},{"id":"https://openalex.org/F4320309872","display_name":"Grantov\u00e1 Agentura, Univerzita Karlova","ror":"https://ror.org/024d6js02"},{"id":"https://openalex.org/F4320321005","display_name":"Ministerstvo \u0160kolstv\u00ed, Ml\u00e1de\u017ee a T\u011blov\u00fdchovy","ror":"https://ror.org/037n8p820"},{"id":"https://openalex.org/F4320321006","display_name":"Grantov\u00e1 Agentura \u010cesk\u00e9 Republiky","ror":"https://ror.org/01pv73b02"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7113901839.pdf","grobid_xml":"https://content.openalex.org/works/W7113901839.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W194463696","https://openalex.org/W1995808589","https://openalex.org/W2045777307","https://openalex.org/W2556468274","https://openalex.org/W2791506886","https://openalex.org/W2804171113","https://openalex.org/W2887981960","https://openalex.org/W2950200056","https://openalex.org/W2999309192","https://openalex.org/W3110897509","https://openalex.org/W3146944767","https://openalex.org/W3177500196","https://openalex.org/W3177828909","https://openalex.org/W3195375135","https://openalex.org/W3211795435","https://openalex.org/W4225552973","https://openalex.org/W4283326616","https://openalex.org/W4307232568","https://openalex.org/W4310733867","https://openalex.org/W4317661995","https://openalex.org/W4322732093","https://openalex.org/W4327550249","https://openalex.org/W4390971193","https://openalex.org/W4392907675","https://openalex.org/W4399849668","https://openalex.org/W4401966068","https://openalex.org/W4404226808","https://openalex.org/W4405531686","https://openalex.org/W4410444270","https://openalex.org/W4412805034","https://openalex.org/W6892920195"],"related_works":[],"abstract_inverted_index":{"Identifying":[0],"protein":[1,54,68,77,118],"binding":[2,16,135,171],"sites":[3,17,136],"is":[4,62],"essential":[5],"for":[6,168],"understanding":[7],"biological":[8],"processes":[9],"and":[10,184],"advancing":[11],"drug":[12],"discovery.":[13],"However,":[14],"cryptic":[15,124,170],"-":[18,29],"transient":[19],"or":[20],"hidden":[21],"pockets":[22],"that":[23],"emerge":[24],"only":[25],"under":[26],"certain":[27],"conditions":[28],"pose":[30],"a":[31,81,90,120],"significant":[32],"challenge":[33],"due":[34],"to":[35,45,100,116,137,150],"their":[36,173],"conformational":[37],"flexibility.":[38],"Traditional":[39],"structure-based":[40],"prediction":[41,105,153],"methods":[42],"often":[43],"fail":[44],"detect":[46],"these":[47],"sites,":[48,172],"as":[49],"they":[50],"rely":[51],"on":[52,75],"rigid":[53],"conformations.":[55],"Therefore,":[56],"the":[57,98,102,114,152],"focus":[58],"of":[59,92,104,123,133],"this":[60],"study":[61],"directed":[63],"towards":[64],"sequence-based":[65,163],"approaches,":[66],"especially":[67],"language":[69],"models,":[70],"which":[71],"do":[72],"not":[73],"depend":[74],"particular":[76],"conformation.":[78],"Starting":[79],"with":[80],"baseline":[82,99],"method":[83],"utilizing":[84],"simple":[85],"transfer":[86],"learning,":[87],"we":[88,128,147],"explore":[89],"range":[91],"finetuning":[93,182],"strategies,":[94],"each":[95],"evaluated":[96],"against":[97],"assess":[101],"improvement":[103],"performance.":[106,141],"We":[107],"incorporate":[108],"multi-task":[109],"learning":[110],"by":[111],"jointly":[112],"training":[113],"model":[115,140],"predict":[117],"flexibility,":[119],"key":[121,156],"characteristic":[122],"sites.":[125],"More":[126],"importantly,":[127],"leverage":[129],"data":[130,185],"from":[131],"datasets":[132],"general":[134],"further":[138],"enhance":[139],"With":[142],"properly":[143],"selected":[144,181],"fine-tuning":[145],"techniques,":[146],"were":[148],"able":[149],"improve":[151],"across":[154],"all":[155],"metrics.":[157],"Our":[158],"results":[159],"demonstrate":[160],"that,":[161],"while":[162],"models":[164],"hold":[165],"strong":[166],"potential":[167],"uncovering":[169],"performance":[174],"can":[175],"be":[176],"significantly":[177],"enhanced":[178],"through":[179],"carefully":[180],"strategies":[183],"sources.":[186]},"counts_by_year":[{"year":2026,"cited_by_count":3}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-12-11T00:00:00"}
