{"id":"https://openalex.org/W3185564986","doi":"https://doi.org/10.1021/acs.jcim.1c00155","title":"DrugPred_RNA\u2014A Tool for Structure-Based Druggability Predictions for RNA Binding Sites","display_name":"DrugPred_RNA\u2014A Tool for Structure-Based Druggability Predictions for RNA Binding Sites","publication_year":2021,"publication_date":"2021-07-21","ids":{"openalex":"https://openalex.org/W3185564986","doi":"https://doi.org/10.1021/acs.jcim.1c00155","mag":"3185564986","pmid":"https://pubmed.ncbi.nlm.nih.gov/34286972"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.1c00155","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c00155","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1021/acs.jcim.1c00155","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058056725","display_name":"Illimar Hugo Rekand","orcid":"https://orcid.org/0000-0002-0457-8024"},"institutions":[{"id":"https://openalex.org/I4432739","display_name":"University of Bergen","ror":"https://ror.org/03zga2b32","country_code":"NO","type":"education","lineage":["https://openalex.org/I4432739"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Illimar Hugo Rekand","raw_affiliation_strings":["Department of Biomedicine, University of Bergen, Jonas Lies Vei, 5020 Bergen, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedicine, University of Bergen, Jonas Lies Vei, 5020 Bergen, Norway","institution_ids":["https://openalex.org/I4432739"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036784729","display_name":"Ruth Brenk","orcid":"https://orcid.org/0000-0002-6204-5488"},"institutions":[{"id":"https://openalex.org/I4432739","display_name":"University of Bergen","ror":"https://ror.org/03zga2b32","country_code":"NO","type":"education","lineage":["https://openalex.org/I4432739"]}],"countries":["NO"],"is_corresponding":true,"raw_author_name":"Ruth Brenk","raw_affiliation_strings":["Department of Biomedicine, University of Bergen, Jonas Lies Vei, 5020 Bergen, Norway"],"raw_orcid":"https://orcid.org/0000-0002-6204-5488","affiliations":[{"raw_affiliation_string":"Department of Biomedicine, University of Bergen, Jonas Lies Vei, 5020 Bergen, Norway","institution_ids":["https://openalex.org/I4432739"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5036784729"],"corresponding_institution_ids":["https://openalex.org/I4432739"],"apc_list":null,"apc_paid":null,"fwci":0.8142,"has_fulltext":false,"cited_by_count":23,"citation_normalized_percentile":{"value":0.71061162,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"61","issue":"8","first_page":"4068","last_page":"4081"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"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":0.9976999759674072,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9950000047683716,"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":0.9915344715118408},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.8301863670349121},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.653754472732544},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.5752811431884766},{"id":"https://openalex.org/keywords/rna-binding-protein","display_name":"RNA-binding protein","score":0.5476067662239075},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.5438646674156189},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4049288332462311},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.34193113446235657},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.29370373487472534},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10633409023284912}],"concepts":[{"id":"https://openalex.org/C10679952","wikidata":"https://www.wikidata.org/wiki/Q5308937","display_name":"Druggability","level":3,"score":0.9915344715118408},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.8301863670349121},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.653754472732544},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.5752811431884766},{"id":"https://openalex.org/C41282012","wikidata":"https://www.wikidata.org/wiki/Q3928341","display_name":"RNA-binding protein","level":4,"score":0.5476067662239075},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.5438646674156189},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4049288332462311},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.34193113446235657},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.29370373487472534},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10633409023284912}],"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":"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":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1021/acs.jcim.1c00155","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c00155","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:34286972","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34286972","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},{"id":"pmh:oai:bora.uib.no:11250/2990173","is_oa":true,"landing_page_url":"https://hdl.handle.net/11250/2990173","pdf_url":null,"source":{"id":"https://openalex.org/S4306401716","display_name":"Duo Research Archive (University of Oslo)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I184942183","host_organization_name":"University of Oslo","host_organization_lineage":["https://openalex.org/I184942183"],"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":"Journal of Chemical Information and Modeling","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8389535","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8389535","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 Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.1c00155","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c00155","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Reduced inequalities","score":0.6600000262260437,"id":"https://metadata.un.org/sdg/10"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":57,"referenced_works":["https://openalex.org/W1906610597","https://openalex.org/W1931081986","https://openalex.org/W1997655258","https://openalex.org/W1999403133","https://openalex.org/W2001568863","https://openalex.org/W2008525757","https://openalex.org/W2009227097","https://openalex.org/W2013779315","https://openalex.org/W2014430663","https://openalex.org/W2030753552","https://openalex.org/W2034549041","https://openalex.org/W2036884070","https://openalex.org/W2044703506","https://openalex.org/W2056589536","https://openalex.org/W2066143642","https://openalex.org/W2068051461","https://openalex.org/W2068351024","https://openalex.org/W2081886031","https://openalex.org/W2084266282","https://openalex.org/W2103564235","https://openalex.org/W2104897337","https://openalex.org/W2106886734","https://openalex.org/W2111307988","https://openalex.org/W2114162221","https://openalex.org/W2114370367","https://openalex.org/W2114850508","https://openalex.org/W2119704253","https://openalex.org/W2130479394","https://openalex.org/W2165509651","https://openalex.org/W2253581743","https://openalex.org/W2275367538","https://openalex.org/W2295598076","https://openalex.org/W2314179822","https://openalex.org/W2394560650","https://openalex.org/W2426348084","https://openalex.org/W2500362036","https://openalex.org/W2502698579","https://openalex.org/W2513799405","https://openalex.org/W2558217333","https://openalex.org/W2560808776","https://openalex.org/W2582743722","https://openalex.org/W2596340280","https://openalex.org/W2612690371","https://openalex.org/W2747225324","https://openalex.org/W2751932844","https://openalex.org/W2756459434","https://openalex.org/W2765760205","https://openalex.org/W2820941669","https://openalex.org/W2913187347","https://openalex.org/W2931878065","https://openalex.org/W2979630284","https://openalex.org/W3022298391","https://openalex.org/W3048003293","https://openalex.org/W3085874984","https://openalex.org/W3102476541","https://openalex.org/W3119808766","https://openalex.org/W4399576823"],"related_works":["https://openalex.org/W2556855892","https://openalex.org/W4214810602","https://openalex.org/W2523769397","https://openalex.org/W1969888071","https://openalex.org/W2035422779","https://openalex.org/W2925167008","https://openalex.org/W3023385275","https://openalex.org/W2008033400","https://openalex.org/W1972982874","https://openalex.org/W3097054638"],"abstract_inverted_index":{"RNA":[0,14,41,50,70,95,111,152],"is":[1,132],"an":[2,110],"emerging":[3],"target":[4],"for":[5,10,68,86,93,151],"drug":[6,148],"discovery.":[7],"However,":[8],"like":[9],"proteins,":[11],"not":[12],"all":[13],"binding":[15,42,51,73,84,96,141],"sites":[16,85,97,142],"are":[17],"equally":[18],"suited":[19],"to":[20,38,45,119,125,146],"be":[21,66,120],"addressed":[22],"with":[23,100],"conventional":[24],"drug-like":[25,106],"ligands.":[26],"To":[27],"this":[28],"end,":[29],"we":[30],"have":[31],"developed":[32],"the":[33,46,53,87,126,140],"structure-based":[34],"druggability":[35],"predictor":[36,54],"DrugPred_RNA":[37,75],"identify":[39],"druggable":[40,80,83],"sites.":[43,74],"Due":[44],"paucity":[47],"of":[48,128],"annotated":[49],"sites,":[52],"was":[55],"trained":[56],"on":[57],"protein":[58,72,88],"pockets,":[59],"albeit":[60],"using":[61],"only":[62],"descriptors":[63],"that":[64,98],"can":[65,144],"calculated":[67],"both":[69],"and":[71,90,136,143],"performed":[76],"well":[77],"in":[78,109,116,139],"discriminating":[79],"from":[81],"less":[82],"set":[89,113],"delivered":[91],"predictions":[92],"selected":[94],"agreed":[99],"manual":[101],"assignment.":[102],"In":[103],"addition,":[104],"most":[105],"ligands":[107],"contained":[108],"test":[112],"were":[114],"found":[115],"pockets":[117],"predicted":[118],"druggable,":[121],"further":[122],"adding":[123],"confidence":[124],"performance":[127],"DrugPred_RNA.":[129],"The":[130],"method":[131],"robust":[133],"against":[134],"conformational":[135],"sequence":[137],"changes":[138],"contribute":[145],"direct":[147],"discovery":[149],"efforts":[150],"targets.":[153]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1}],"updated_date":"2026-06-10T14:10:52.464848","created_date":"2025-10-10T00:00:00"}