{"id":"https://openalex.org/W4390971193","doi":"https://doi.org/10.1109/bibm58861.2023.10385497","title":"Cryptic binding site prediction with protein language models","display_name":"Cryptic binding site prediction with protein language models","publication_year":2023,"publication_date":"2023-12-05","ids":{"openalex":"https://openalex.org/W4390971193","doi":"https://doi.org/10.1109/bibm58861.2023.10385497"},"language":"en","primary_location":{"id":"doi:10.1109/bibm58861.2023.10385497","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm58861.2023.10385497","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5009850391","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":true,"raw_author_name":"V\u00edt \u0160krh\u00e1k","raw_affiliation_strings":["Charles University,Faculty of Mathematics and Physics,Department of Software Engineering,Prague,Czech Republic","Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic"],"affiliations":[{"raw_affiliation_string":"Charles University,Faculty of Mathematics and Physics,Department of Software Engineering,Prague,Czech Republic","institution_ids":["https://openalex.org/I21250087"]},{"raw_affiliation_string":"Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic","institution_ids":["https://openalex.org/I21250087"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069572460","display_name":"Mari\u00e1n Novotn\u00fd","orcid":"https://orcid.org/0000-0001-8788-3202"},"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":"Marian Novotn\u00fd","raw_affiliation_strings":["Charles University,Faculty of Science,Department of Cell Biology,Prague,Czech Republic","Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic"],"affiliations":[{"raw_affiliation_string":"Charles University,Faculty of Science,Department of Cell Biology,Prague,Czech Republic","institution_ids":["https://openalex.org/I21250087"]},{"raw_affiliation_string":"Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic","institution_ids":["https://openalex.org/I21250087"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019110655","display_name":"Kamila Riedlov\u00e1","orcid":"https://orcid.org/0000-0002-9134-2297"},"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":"Kamila Riedlova","raw_affiliation_strings":["Charles University,Faculty of Mathematics and Physics,Department of Software Engineering,Prague,Czech Republic","Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic"],"affiliations":[{"raw_affiliation_string":"Charles University,Faculty of Mathematics and Physics,Department of Software Engineering,Prague,Czech Republic","institution_ids":["https://openalex.org/I21250087"]},{"raw_affiliation_string":"Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic","institution_ids":["https://openalex.org/I21250087"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049617942","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,Faculty of Mathematics and Physics,Department of Software Engineering,Prague,Czech Republic","Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic"],"affiliations":[{"raw_affiliation_string":"Charles University,Faculty of Mathematics and Physics,Department of Software Engineering,Prague,Czech Republic","institution_ids":["https://openalex.org/I21250087"]},{"raw_affiliation_string":"Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic","institution_ids":["https://openalex.org/I21250087"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5009850391"],"corresponding_institution_ids":["https://openalex.org/I21250087"],"apc_list":null,"apc_paid":null,"fwci":1.6136,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.86527952,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":null,"issue":null,"first_page":"2883","last_page":"2888"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9993000030517578,"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":0.9993000030517578,"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/T13326","display_name":"Biochemical and Structural Characterization","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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.998199999332428,"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":0.6480301022529602},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5520369410514832},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.5087199807167053},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5061623454093933},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.44655269384384155},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4314410090446472},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4016752243041992},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.33365100622177124},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.20518580079078674},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1541474461555481}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6480301022529602},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5520369410514832},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.5087199807167053},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5061623454093933},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.44655269384384155},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4314410090446472},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4016752243041992},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.33365100622177124},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.20518580079078674},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1541474461555481},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm58861.2023.10385497","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm58861.2023.10385497","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320311687","display_name":"Ministry of Education","ror":"https://ror.org/03m01yf64"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W2102461176","https://openalex.org/W2114850508","https://openalex.org/W2145023212","https://openalex.org/W2163352757","https://openalex.org/W2164088236","https://openalex.org/W2265102996","https://openalex.org/W2617750324","https://openalex.org/W2767813457","https://openalex.org/W2804171113","https://openalex.org/W2887981960","https://openalex.org/W2990453062","https://openalex.org/W3012511738","https://openalex.org/W3078303041","https://openalex.org/W3146944767","https://openalex.org/W3157437194","https://openalex.org/W4211054902","https://openalex.org/W4213072029","https://openalex.org/W4283011532","https://openalex.org/W4287724045","https://openalex.org/W4313527276","https://openalex.org/W4317754139","https://openalex.org/W4322732093","https://openalex.org/W4385838908","https://openalex.org/W6631190155","https://openalex.org/W6730169791","https://openalex.org/W6780145172","https://openalex.org/W6855929460","https://openalex.org/W6925204217"],"related_works":["https://openalex.org/W2898732673","https://openalex.org/W2410053581","https://openalex.org/W2383658677","https://openalex.org/W3123203398","https://openalex.org/W2355466661","https://openalex.org/W2961085424","https://openalex.org/W1968459159","https://openalex.org/W1972473893","https://openalex.org/W2466435674","https://openalex.org/W2025584407"],"abstract_inverted_index":{"Structure-based":[0],"identification":[1],"of":[2,14,65,74,123],"protein-ligand":[3],"binding":[4,52,58,96],"sites":[5,53],"plays":[6],"a":[7,29,66,113],"crucial":[8],"role":[9],"in":[10,62,93,112],"the":[11,27,57,63,72,94,121],"initial":[12],"stages":[13],"rational":[15],"drug":[16],"discovery":[17],"pipelines.":[18],"As":[19],"machine":[20],"learning":[21],"methods":[22,48],"are":[23,40,103],"increasingly":[24],"integrated":[25],"into":[26],"process,":[28],"significant":[30],"challenge":[31],"arises":[32],"while":[33],"training":[34],"these":[35,47],"methods,":[36,89],"as":[37],"labeled":[38],"data":[39],"typically":[41],"derived":[42],"from":[43],"ligand-bound":[44],"structures.":[45],"Consequently,":[46],"struggle":[49],"to":[50,79,119],"detect":[51],"within":[54],"proteins":[55],"where":[56],"site":[59,97],"is":[60],"concealed":[61],"absence":[64],"bound":[67],"ligand.":[68],"Here,":[69],"we":[70],"explore":[71],"possibility":[73],"harnessing":[75],"protein":[76],"language":[77],"models":[78,111],"address":[80],"this":[81],"issue":[82],"and":[83,100],"compare":[84],"their":[85],"performance":[86],"against":[87],"state-of-the-art":[88,122],"both":[90],"those":[91,101],"specialized":[92],"cryptic":[95],"(CBS)":[98],"detection":[99],"that":[102,107],"not.":[104],"We":[105],"show":[106],"applying":[108],"pre-trained":[109],"protein-language":[110],"relatively":[114],"straightforward":[115],"manner":[116],"enables":[117],"us":[118],"surpass":[120],"CBS":[124],"prediction.":[125]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
