{"id":"https://openalex.org/W4307035489","doi":"https://doi.org/10.1021/acs.jcim.2c00947","title":"ProBiS-Fold Approach for Annotation of Human Structures from the AlphaFold Database with No Corresponding Structure in the PDB to Discover New Druggable Binding Sites","display_name":"ProBiS-Fold Approach for Annotation of Human Structures from the AlphaFold Database with No Corresponding Structure in the PDB to Discover New Druggable Binding Sites","publication_year":2022,"publication_date":"2022-10-21","ids":{"openalex":"https://openalex.org/W4307035489","doi":"https://doi.org/10.1021/acs.jcim.2c00947","pmid":"https://pubmed.ncbi.nlm.nih.gov/36269348"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.2c00947","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c00947","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5007997462","display_name":"Janez Konc","orcid":"https://orcid.org/0000-0003-0160-3375"},"institutions":[{"id":"https://openalex.org/I4210152560","display_name":"National Institute of Chemistry","ror":"https://ror.org/050mac570","country_code":"SI","type":"facility","lineage":["https://openalex.org/I4210152560"]}],"countries":["SI"],"is_corresponding":true,"raw_author_name":"Janez Konc","raw_affiliation_strings":["Theory Department, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia"],"raw_orcid":"https://orcid.org/0000-0003-0160-3375","affiliations":[{"raw_affiliation_string":"Theory Department, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia","institution_ids":["https://openalex.org/I4210152560"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074495088","display_name":"Du\u0161anka Jane\u017ei\u010d","orcid":"https://orcid.org/0000-0003-4067-0116"},"institutions":[{"id":"https://openalex.org/I118905719","display_name":"University of Primorska","ror":"https://ror.org/05xefg082","country_code":"SI","type":"education","lineage":["https://openalex.org/I118905719"]}],"countries":["SI"],"is_corresponding":true,"raw_author_name":"Du\u0161anka Jane\u017ei\u010d","raw_affiliation_strings":["Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagolja\u0161ka 8, SI-6000 Koper, Slovenia"],"raw_orcid":"https://orcid.org/0000-0003-4067-0116","affiliations":[{"raw_affiliation_string":"Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagolja\u0161ka 8, SI-6000 Koper, Slovenia","institution_ids":["https://openalex.org/I118905719"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5007997462","https://openalex.org/A5074495088"],"corresponding_institution_ids":["https://openalex.org/I118905719","https://openalex.org/I4210152560"],"apc_list":null,"apc_paid":null,"fwci":2.2579,"has_fulltext":false,"cited_by_count":19,"citation_normalized_percentile":{"value":0.8955042,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"62","issue":"22","first_page":"5821","last_page":"5829"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9994999766349792,"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":0.9994999766349792,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9952999949455261,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9939000010490417,"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/druggability","display_name":"Druggability","score":0.827680766582489},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.8192266821861267},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6707360744476318},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5241242051124573},{"id":"https://openalex.org/keywords/fold","display_name":"Fold (higher-order function)","score":0.4544151723384857},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4356743097305298},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3606128692626953},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.30787375569343567},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2550804615020752},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2528444528579712},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.13729333877563477},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.12317031621932983},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.0669705867767334}],"concepts":[{"id":"https://openalex.org/C10679952","wikidata":"https://www.wikidata.org/wiki/Q5308937","display_name":"Druggability","level":3,"score":0.827680766582489},{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.8192266821861267},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6707360744476318},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5241242051124573},{"id":"https://openalex.org/C53942344","wikidata":"https://www.wikidata.org/wiki/Q951651","display_name":"Fold (higher-order function)","level":2,"score":0.4544151723384857},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4356743097305298},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3606128692626953},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.30787375569343567},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2550804615020752},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2528444528579712},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.13729333877563477},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.12317031621932983},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0669705867767334},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.2c00947","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c00947","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:36269348","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36269348","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 chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2070509478","display_name":"Protein interaction atlas for prediction of genetic variations involved in drug interactions and disease development","funder_award_id":"J1-1715","funder_id":"https://openalex.org/F4320322554","funder_display_name":"Javna Agencija za Raziskovalno Dejavnost RS"},{"id":"https://openalex.org/G4294235106","display_name":"New computational tools at the PDB scale for drug discovery","funder_award_id":"J1-9186","funder_id":"https://openalex.org/F4320322554","funder_display_name":"Javna Agencija za Raziskovalno Dejavnost RS"},{"id":"https://openalex.org/G4652101948","display_name":"COGEVAB: New COmputational tools at the molecular scale for studying effects of GEnetic VAriants on drug Binding","funder_award_id":"N1-0142","funder_id":"https://openalex.org/F4320322554","funder_display_name":"Javna Agencija za Raziskovalno Dejavnost RS"},{"id":"https://openalex.org/G6946677552","display_name":"Novi pristopi za bolj\u0161a biolo\u0161ka zdravila (Slovene)","funder_award_id":"L7-8269","funder_id":"https://openalex.org/F4320322554","funder_display_name":"Javna Agencija za Raziskovalno Dejavnost RS"},{"id":"https://openalex.org/G7168838956","display_name":"Tools for innovative drug design","funder_award_id":"N1-0209","funder_id":"https://openalex.org/F4320322554","funder_display_name":"Javna Agencija za Raziskovalno Dejavnost RS"}],"funders":[{"id":"https://openalex.org/F4320322554","display_name":"Javna Agencija za Raziskovalno Dejavnost RS","ror":"https://ror.org/059bp8k51"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":35,"referenced_works":["https://openalex.org/W1968319881","https://openalex.org/W1988166955","https://openalex.org/W2024685656","https://openalex.org/W2044703506","https://openalex.org/W2106449850","https://openalex.org/W2138770756","https://openalex.org/W2165535543","https://openalex.org/W2286147449","https://openalex.org/W2322633051","https://openalex.org/W2399060478","https://openalex.org/W2552388238","https://openalex.org/W2554746068","https://openalex.org/W2586096628","https://openalex.org/W2588309452","https://openalex.org/W2613478649","https://openalex.org/W2767891136","https://openalex.org/W2769925250","https://openalex.org/W2772720275","https://openalex.org/W2898364362","https://openalex.org/W2899070097","https://openalex.org/W2900167333","https://openalex.org/W2900674118","https://openalex.org/W2937705502","https://openalex.org/W2939950131","https://openalex.org/W2947525400","https://openalex.org/W2992752586","https://openalex.org/W3112376646","https://openalex.org/W3177828909","https://openalex.org/W3185701646","https://openalex.org/W3208408872","https://openalex.org/W3211795435","https://openalex.org/W4200585917","https://openalex.org/W4223432929","https://openalex.org/W4282939988","https://openalex.org/W4285020367"],"related_works":["https://openalex.org/W2556855892","https://openalex.org/W4280541024","https://openalex.org/W4214810602","https://openalex.org/W2523769397","https://openalex.org/W2000687555","https://openalex.org/W2158546283","https://openalex.org/W2255897055","https://openalex.org/W2013600324","https://openalex.org/W4307035489","https://openalex.org/W2538996250"],"abstract_inverted_index":{"ProBiS":[0,42],"(Protein":[1],"Binding":[2],"Sites),":[3],"a":[4,26],"local":[5],"structure-based":[6],"comparison":[7],"algorithm,":[8],"is":[9,44,197],"used":[10,45],"in":[11,29,72,80,86,174],"the":[12,22,30,54,58,62,73,81,100,125,156,175],"new":[13,37,165],"ProBiS-Fold":[14,148],"web":[15,195],"server":[16,196],"to":[17,35,46,64,95,130,135,139,183,200],"annotate":[18],"human":[19,158],"structures":[20,60],"from":[21,61,99],"AlphaFold":[23,55,82,101,113],"database":[24],"without":[25],"corresponding":[27,172],"structure":[28,51,173],"Protein":[31],"Data":[32],"Bank":[33],"(PDB)":[34],"discover":[36],"druggable":[38,166],"binding":[39,69,78,104,117,153,167],"sites.":[40],"The":[41,194],"algorithm":[43],"compare":[47],"each":[48,96],"query":[49,97],"protein":[50,59,98,185],"predicted":[52],"by":[53],"approach":[56],"with":[57],"PDB":[63,74,90],"identify":[65],"similarities":[66],"between":[67],"known":[68,131],"sites":[70,79,91,105,118,154,168],"found":[71],"and":[75,103,142,151,189],"yet":[76],"unknown":[77],"database.":[83],"Ligands":[84],"bound":[85],"these":[87],"identified":[88,107],"similar":[89],"are":[92,106,119],"then":[93],"transferred":[94],"database,":[102],"as":[108],"ligand":[109],"clusters":[110],"on":[111,124],"an":[112],"protein.":[114],"Small":[115],"molecule":[116],"assigned":[120],"druggability":[121],"scores":[122],"based":[123],"similarity":[126],"of":[127],"their":[128,140],"ligands":[129],"drugs,":[132],"allowing":[133],"them":[134],"be":[136],"ranked":[137],"according":[138],"perceived":[141],"actual":[143],"potential":[144],"for":[145,155],"drug":[146,191],"development.":[147],"provides":[149],"interactive":[150],"downloadable":[152],"entire":[157],"structural":[159],"proteome,":[160],"including":[161],"more":[162],"than":[163],"3000":[164],"that":[169],"have":[170],"no":[171],"PDB,":[176],"taking":[177],"into":[178],"account":[179],"AlphaFold's":[180],"model":[181],"quality,":[182],"enable":[184],"structure-function":[186],"relationship":[187],"studies":[188],"pharmaceutical":[190],"discovery":[192],"research.":[193],"freely":[198],"accessible":[199],"academic":[201],"users":[202],"at":[203],"http://probis-fold.insilab.org.":[204]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":1}],"updated_date":"2026-08-08T01:25:22.217667","created_date":"2025-10-10T00:00:00"}
