{"id":"https://openalex.org/W7171544649","doi":"https://doi.org/10.1145/3807503.3819482","title":"UniPocket: Unified Ligand and Cryptic Pocket Prediction from Protein Language Model Embeddings","display_name":"UniPocket: Unified Ligand and Cryptic Pocket Prediction from Protein Language Model Embeddings","publication_year":2026,"publication_date":"2026-06-30","ids":{"openalex":"https://openalex.org/W7171544649","doi":"https://doi.org/10.1145/3807503.3819482"},"language":null,"primary_location":{"id":"doi:10.1145/3807503.3819482","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3819482","pdf_url":null,"source":null,"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 17th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1145/3807503.3819482","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058546485","display_name":"Lening Zhao","orcid":null},"institutions":[{"id":"https://openalex.org/I4210127693","display_name":"Penn Center for AIDS Research","ror":"https://ror.org/047939x15","country_code":"US","type":"facility","lineage":["https://openalex.org/I102322052","https://openalex.org/I1335321130","https://openalex.org/I4210127693","https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lening Zhao","raw_affiliation_strings":["University of Pennsylvainia, Philadelphia, Pennsylvania, USA"],"raw_orcid":"https://orcid.org/0000-0003-0847-9880","affiliations":[{"raw_affiliation_string":"University of Pennsylvainia, Philadelphia, Pennsylvania, USA","institution_ids":["https://openalex.org/I4210127693"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084521312","display_name":"Tianhua Zhai","orcid":"https://orcid.org/0009-0007-9712-9132"},"institutions":[{"id":"https://openalex.org/I4210127693","display_name":"Penn Center for AIDS Research","ror":"https://ror.org/047939x15","country_code":"US","type":"facility","lineage":["https://openalex.org/I102322052","https://openalex.org/I1335321130","https://openalex.org/I4210127693","https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tianhua Zhai","raw_affiliation_strings":["University of Pennsylvainia, Philadelphia, USA"],"raw_orcid":"https://orcid.org/0009-0007-9712-9132","affiliations":[{"raw_affiliation_string":"University of Pennsylvainia, Philadelphia, USA","institution_ids":["https://openalex.org/I4210127693"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100333320","display_name":"Li Shen","orcid":"https://orcid.org/0000-0002-5443-0503"},"institutions":[{"id":"https://openalex.org/I4210127693","display_name":"Penn Center for AIDS Research","ror":"https://ror.org/047939x15","country_code":"US","type":"facility","lineage":["https://openalex.org/I102322052","https://openalex.org/I1335321130","https://openalex.org/I4210127693","https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Li Shen","raw_affiliation_strings":["University of Pennsylvainia, Philadelphia, Pennsylvania, USA"],"raw_orcid":"https://orcid.org/0000-0002-5443-0503","affiliations":[{"raw_affiliation_string":"University of Pennsylvainia, Philadelphia, Pennsylvania, USA","institution_ids":["https://openalex.org/I4210127693"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I4210127693"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"9"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":null,"topics":[],"keywords":[{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.37130001187324524},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.32280001044273376},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.3158999979496002},{"id":"https://openalex.org/keywords/term","display_name":"Term (time)","score":0.28780001401901245},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.28439998626708984},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.2800999879837036}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5091000199317932},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4260999858379364},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.37130001187324524},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3296000063419342},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.32280001044273376},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.3158999979496002},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.29010000824928284},{"id":"https://openalex.org/C61797465","wikidata":"https://www.wikidata.org/wiki/Q1188986","display_name":"Term (time)","level":2,"score":0.28780001401901245},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2874999940395355},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.28439998626708984},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.28439998626708984},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.2800999879837036},{"id":"https://openalex.org/C2777212361","wikidata":"https://www.wikidata.org/wiki/Q5127848","display_name":"Class (philosophy)","level":2,"score":0.27900001406669617},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.27880001068115234},{"id":"https://openalex.org/C12426560","wikidata":"https://www.wikidata.org/wiki/Q189569","display_name":"Basis (linear algebra)","level":2,"score":0.2637999951839447},{"id":"https://openalex.org/C149364088","wikidata":"https://www.wikidata.org/wiki/Q185917","display_name":"Translation (biology)","level":4,"score":0.2635999917984009}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3807503.3819482","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3819482","pdf_url":null,"source":null,"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 17th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/3807503.3819482","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3819482","pdf_url":null,"source":null,"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 17th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3011192577","display_name":null,"funder_award_id":"R01 AG071470, U01 AG068057, U01 AG066833, U19 AG074879.","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W1975447903","https://openalex.org/W1986159966","https://openalex.org/W1986240377","https://openalex.org/W2031194866","https://openalex.org/W2031390939","https://openalex.org/W2079953901","https://openalex.org/W2162882526","https://openalex.org/W2164088236","https://openalex.org/W2265102996","https://openalex.org/W2343614482","https://openalex.org/W2530847795","https://openalex.org/W2791506886","https://openalex.org/W2887981960","https://openalex.org/W3165603781","https://openalex.org/W3177500196","https://openalex.org/W4322732093","https://openalex.org/W4327550249","https://openalex.org/W4385576721","https://openalex.org/W4391308485","https://openalex.org/W4404226808","https://openalex.org/W4405531686","https://openalex.org/W4406136976","https://openalex.org/W4409774501","https://openalex.org/W4411864018"],"related_works":[],"abstract_inverted_index":{"Identifying":[0],"druggable":[1],"pockets":[2],"in":[3,48],"proteins":[4],"is":[5,34],"central":[6],"to":[7,90,128],"structure-based":[8],"drug":[9],"discovery,":[10],"yet":[11],"conventional":[12,56],"ligand-binding-site":[13,148],"prediction":[14,17,70,144,149],"and":[15,29,57,74,108,117,145],"cryptic-pocket":[16,75,109,143],"are":[18],"typically":[19],"treated":[20],"as":[21,88],"separate":[22],"tasks":[23,160],"requiring":[24],"distinct":[25],"tools,":[26],"preprocessing":[27],"pipelines,":[28],"evaluation":[30],"protocols.":[31],"This":[32],"separation":[33],"limiting":[35],"because":[36],"the":[37,125],"two":[38,96,126],"problems":[39],"share":[40],"a":[41,64,78,91,137],"common":[42],"biological":[43],"foundation:":[44],"co-evolutionary":[45],"patterns":[46],"encoded":[47],"protein":[49],"sequences":[50],"carry":[51],"implicit":[52],"signals":[53],"about":[54],"both":[55,72,159],"cryptic":[58],"binding":[59],"sites.":[60],"We":[61],"present":[62],"UniPocket,":[63],"unified":[65],"multitask":[66],"framework":[67],"for":[68,142,147],"residue-level":[69],"of":[71,140],"ligand-binding":[73],"residues":[76],"within":[77],"single":[79],"shared-backbone":[80],"architecture.":[81],"UniPocket":[82,135],"uses":[83],"frozen":[84],"per-residue":[85],"ESM-2":[86],"embeddings":[87],"input":[89,166],"lightweight":[92],"residual":[93],"MLP":[94],"with":[95],"task-specific":[97],"heads,":[98],"trained":[99],"on":[100,158],"ligand-contact":[101],"labels":[102],"from":[103,111],"recently":[104],"deposited":[105],"PDB":[106],"structures":[107],"annotations":[110],"CryptoBench.":[112],"Training":[113],"alternates":[114],"between":[115],"ligand-labeled":[116],"cryptic-labeled":[118],"mini-batches,":[119],"while":[120],"an":[121],"orthogonality":[122],"regularizer":[123],"encourages":[124],"heads":[127],"learn":[129],"complementary":[130],"rather":[131],"than":[132],"redundant":[133],"signals.":[134],"achieves":[136],"macro":[138],"ROC-AUC":[139],"0.82":[141],"0.76":[146],"\u2014":[150],"matching":[151],"or":[152],"exceeding":[153],"all":[154],"dedicated":[155],"single-task":[156],"baselines":[157],"simultaneously,":[161],"without":[162],"any":[163],"3D":[164],"structural":[165],"at":[167],"inference":[168],"time.":[169]},"counts_by_year":[],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2026-07-29T00:00:00"}
