{"id":"https://openalex.org/W7117139636","doi":"https://doi.org/10.1186/s13321-025-01125-x","title":"The Human Omnibus of Targetable Pockets","display_name":"The Human Omnibus of Targetable Pockets","publication_year":2025,"publication_date":"2025-12-24","ids":{"openalex":"https://openalex.org/W7117139636","doi":"https://doi.org/10.1186/s13321-025-01125-x","pmid":"https://pubmed.ncbi.nlm.nih.gov/41444992"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-025-01125-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01125-x","pdf_url":"https://link.springer.com/content/pdf/10.1186/s13321-025-01125-x.pdf","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://link.springer.com/content/pdf/10.1186/s13321-025-01125-x.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081232063","display_name":"Kristy A. Carpenter","orcid":"https://orcid.org/0000-0003-4570-5170"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Kristy A. Carpenter","raw_affiliation_strings":["Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5121195971","display_name":"Russ B. Altman","orcid":null},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Russ B. Altman","raw_affiliation_strings":["Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA. russ.altman@stanford.edu","Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA. russ.altman@stanford.edu","Department of Genetics, Stanford University, Stanford, CA, 94305, USA. russ.altman@stanford.edu","Department of Medicine, Stanford University, Stanford, CA, 94305, USA. russ.altman@stanford.edu"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA. russ.altman@stanford.edu","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA. russ.altman@stanford.edu","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Department of Genetics, Stanford University, Stanford, CA, 94305, USA. russ.altman@stanford.edu","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Department of Medicine, Stanford University, Stanford, CA, 94305, USA. russ.altman@stanford.edu","institution_ids":["https://openalex.org/I97018004"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5081232063"],"corresponding_institution_ids":["https://openalex.org/I97018004"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":1.348,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.88047799,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"17","issue":"1","first_page":"180","last_page":"180"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.44209998846054077,"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":0.44209998846054077,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.13410000503063202,"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/T11178","display_name":"Receptor Mechanisms and Signaling","score":0.0877000018954277,"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/human-proteome-project","display_name":"Human proteome project","score":0.7142000198364258},{"id":"https://openalex.org/keywords/druggability","display_name":"Druggability","score":0.7116000056266785},{"id":"https://openalex.org/keywords/leverage","display_name":"Leverage (statistics)","score":0.6238999962806702},{"id":"https://openalex.org/keywords/ensembl","display_name":"Ensembl","score":0.4020000100135803},{"id":"https://openalex.org/keywords/drugbank","display_name":"DrugBank","score":0.400299996137619},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.3815999925136566},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.37130001187324524},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.36559998989105225}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7487000226974487},{"id":"https://openalex.org/C94795543","wikidata":"https://www.wikidata.org/wiki/Q3813754","display_name":"Human proteome project","level":4,"score":0.7142000198364258},{"id":"https://openalex.org/C10679952","wikidata":"https://www.wikidata.org/wiki/Q5308937","display_name":"Druggability","level":3,"score":0.7116000056266785},{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.6238999962806702},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.49399998784065247},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4237000048160553},{"id":"https://openalex.org/C141674004","wikidata":"https://www.wikidata.org/wiki/Q1344256","display_name":"Ensembl","level":5,"score":0.4020000100135803},{"id":"https://openalex.org/C155261790","wikidata":"https://www.wikidata.org/wiki/Q1122544","display_name":"DrugBank","level":3,"score":0.400299996137619},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.3815999925136566},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.37130001187324524},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.36559998989105225},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.3427000045776367},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33709999918937683},{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.30149999260902405},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.2973000109195709},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2948000133037567},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2913999855518341},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.28850001096725464},{"id":"https://openalex.org/C2777494893","wikidata":"https://www.wikidata.org/wiki/Q4781752","display_name":"Approved drug","level":3,"score":0.2768000066280365},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.2736999988555908},{"id":"https://openalex.org/C163763905","wikidata":"https://www.wikidata.org/wiki/Q17075943","display_name":"Precision medicine","level":2,"score":0.260699987411499},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.2603999972343445},{"id":"https://openalex.org/C1167327","wikidata":"https://www.wikidata.org/wiki/Q14884140","display_name":"HRAS","level":5,"score":0.25859999656677246}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-025-01125-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01125-x","pdf_url":"https://link.springer.com/content/pdf/10.1186/s13321-025-01125-x.pdf","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:41444992","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41444992","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 cheminformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:644e7d6660b24ecba460e4129ade07de","is_oa":true,"landing_page_url":"https://doaj.org/article/644e7d6660b24ecba460e4129ade07de","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":"Journal of Cheminformatics, Vol 17, Iss 1, Pp 1-24 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12729103","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12729103/","pdf_url":null,"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":"J Cheminform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13321-025-01125-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01125-x","pdf_url":"https://link.springer.com/content/pdf/10.1186/s13321-025-01125-x.pdf","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1743763002","display_name":null,"funder_award_id":"R01GM102365","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G3729213239","display_name":null,"funder_award_id":"GRFP DGE-1656518","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8111674771","display_name":null,"funder_award_id":"F31GM151783","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G8668739158","display_name":null,"funder_award_id":"T15LM007033","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320334432","display_name":"Stanford Research Computing Center, Stanford University","ror":null},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7117139636.pdf","grobid_xml":"https://content.openalex.org/works/W7117139636.grobid-xml"},"referenced_works_count":93,"referenced_works":["https://openalex.org/W1975447903","https://openalex.org/W1983194490","https://openalex.org/W2004175162","https://openalex.org/W2007624258","https://openalex.org/W2018661561","https://openalex.org/W2043580883","https://openalex.org/W2073746700","https://openalex.org/W2105902442","https://openalex.org/W2112109058","https://openalex.org/W2114930488","https://openalex.org/W2123440974","https://openalex.org/W2128339707","https://openalex.org/W2130479394","https://openalex.org/W2132395520","https://openalex.org/W2133990057","https://openalex.org/W2146926552","https://openalex.org/W2156575953","https://openalex.org/W2164088236","https://openalex.org/W2169678694","https://openalex.org/W2177550115","https://openalex.org/W2474188283","https://openalex.org/W2543342371","https://openalex.org/W2554651637","https://openalex.org/W2764265682","https://openalex.org/W2809686546","https://openalex.org/W2882976371","https://openalex.org/W2887981960","https://openalex.org/W2895884529","https://openalex.org/W2948831670","https://openalex.org/W2963086398","https://openalex.org/W2980948514","https://openalex.org/W2992613109","https://openalex.org/W3005694381","https://openalex.org/W3007743886","https://openalex.org/W3009999522","https://openalex.org/W3169464554","https://openalex.org/W3177828909","https://openalex.org/W3183475563","https://openalex.org/W3185701646","https://openalex.org/W3209056694","https://openalex.org/W3215525389","https://openalex.org/W4210742550","https://openalex.org/W4211238337","https://openalex.org/W4213042275","https://openalex.org/W4223413162","https://openalex.org/W4231059664","https://openalex.org/W4245357560","https://openalex.org/W4255677297","https://openalex.org/W4282939988","https://openalex.org/W4306353170","https://openalex.org/W4306937122","https://openalex.org/W4307035489","https://openalex.org/W4308616064","https://openalex.org/W4309506674","https://openalex.org/W4320494012","https://openalex.org/W4322732093","https://openalex.org/W4327550249","https://openalex.org/W4366606490","https://openalex.org/W4368373587","https://openalex.org/W4376131123","https://openalex.org/W4385407166","https://openalex.org/W4386457661","https://openalex.org/W4386758612","https://openalex.org/W4387866453","https://openalex.org/W4389174567","https://openalex.org/W4389696354","https://openalex.org/W4390734415","https://openalex.org/W4391075279","https://openalex.org/W4392544734","https://openalex.org/W4393128461","https://openalex.org/W4394931737","https://openalex.org/W4396721167","https://openalex.org/W4396870607","https://openalex.org/W4399567091","https://openalex.org/W4399940463","https://openalex.org/W4400279603","https://openalex.org/W4401455214","https://openalex.org/W4402801121","https://openalex.org/W4403324307","https://openalex.org/W4403394716","https://openalex.org/W4403514887","https://openalex.org/W4404103762","https://openalex.org/W4404226808","https://openalex.org/W4404228356","https://openalex.org/W4404565424","https://openalex.org/W4404797932","https://openalex.org/W4405090494","https://openalex.org/W4405531686","https://openalex.org/W4406274436","https://openalex.org/W4406341111","https://openalex.org/W4406630424","https://openalex.org/W4406795926","https://openalex.org/W4407688507"],"related_works":[],"abstract_inverted_index":{"Hundreds":[0],"of":[1,13,53,66,72,108],"computational":[2],"methods":[3,59,101],"for":[4,24],"predicting":[5],"ligand":[6,142],"binding":[7,143],"pockets":[8,16,43,77,127,192],"exist,":[9],"but":[10],"the":[11,18,63,79,109,130,171,177,196,203,207],"problem":[12],"finding":[14],"druggable":[15,191],"throughout":[17],"human":[19,81,111],"proteome":[20,82],"persists.":[21],"Different":[22],"strategies":[23,38],"pocket-finding":[25,37,58,100],"excel":[26],"in":[27,154],"different":[28,36],"use":[29],"cases.":[30],"Ensemble":[31],"models":[32],"that":[33,83],"leverage":[34],"multiple":[35,57],"can":[39],"best":[40],"capture":[41],"diverse":[42],"at":[44],"scale.":[45],"Despite":[46],"this,":[47],"no":[48],"publicly":[49],"available":[50],"human-proteome-wide":[51],"datasets":[52],"pocket":[54,117,152],"predictions":[55],"from":[56,150],"exist.":[60],"We":[61,91,113,200],"present":[62],"Human":[64],"Omnibus":[65],"Targetable":[67],"Pockets":[68],"(HOTPocket),":[69],"a":[70,115],"dataset":[71,94,205],"over":[73,78,102],"2.4":[74],"million":[75],"predicted":[76],"entire":[80],"utilizes":[84],"both":[85,202],"experimentally-determined":[86],"and":[87,105,128,167,181,195,206],"computationally-predicted":[88],"protein":[89],"structures.":[90],"assembled":[92],"this":[93],"by":[95],"running":[96],"seven":[97],"diverse,":[98],"established":[99],"all":[103,162],"PDB":[104],"AlphaFold2":[106],"structures":[107],"canonical":[110],"proteome.":[112],"created":[114],"novel":[116],"scoring":[118],"method,":[119],"hotpocketNN,":[120],"which":[121,147],"we":[122],"used":[123],"to":[124,139,188],"filter":[125],"candidate":[126],"assemble":[129],"final":[131],"proteome-wide":[132],"dataset.":[133,183],"Our":[134],"hotpocketNN":[135,159,185,208],"method":[136,160,209],"is":[137],"able":[138,187],"recover":[140],"known":[141],"pockets,":[144],"including":[145,165],"those":[146],"are":[148],"dissimilar":[149],"any":[151],"seen":[153],"its":[155],"training":[156],"set.":[157],"The":[158],"outperforms":[161],"constituent":[163],"methods,":[164],"P2Rank":[166],"Fpocket,":[168],"when":[169],"assessing":[170],"precision":[172],"with":[173],"DCA":[174],"criterion":[175],"on":[176,193],"Astex":[178],"Diverse":[179],"Set":[180],"PoseBusters":[182],"Additionally,":[184],"was":[186],"identify":[189],"recently-discovered":[190],"KRAS":[194],"mu":[197],"opioid":[198],"receptor.":[199],"make":[201],"HOTPocket":[204],"freely":[210],"available.":[211]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-12-24T00:00:00"}