{"id":"https://openalex.org/W7139098357","doi":"https://doi.org/10.1021/acs.jcim.5c02955","title":"Critical Assessment of a Structure-Based Pipeline for Targeting the Long Noncoding RNA MALAT1","display_name":"Critical Assessment of a Structure-Based Pipeline for Targeting the Long Noncoding RNA MALAT1","publication_year":2026,"publication_date":"2026-03-19","ids":{"openalex":"https://openalex.org/W7139098357","doi":"https://doi.org/10.1021/acs.jcim.5c02955","pmid":"https://pubmed.ncbi.nlm.nih.gov/41855101"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c02955","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c02955","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.5c02955","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5060583929","display_name":"Riccardo Aguti","orcid":"https://orcid.org/0000-0003-2202-2000"},"institutions":[{"id":"https://openalex.org/I2799787213","display_name":"Alma Mater Europaea","ror":"https://ror.org/028a67802","country_code":"SI","type":"education","lineage":["https://openalex.org/I2799787213"]},{"id":"https://openalex.org/I30771326","display_name":"Italian Institute of Technology","ror":"https://ror.org/042t93s57","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326"]},{"id":"https://openalex.org/I4210138427","display_name":"Computational Physics (United States)","ror":"https://ror.org/03grsxg62","country_code":"US","type":"company","lineage":["https://openalex.org/I4210138427"]},{"id":"https://openalex.org/I9360294","display_name":"University of Bologna","ror":"https://ror.org/01111rn36","country_code":"IT","type":"education","lineage":["https://openalex.org/I9360294"]}],"countries":["IT","SI","US"],"is_corresponding":false,"raw_author_name":"Riccardo Aguti","raw_affiliation_strings":["Computational and Chemical Biology","Department of Pharmacy and Biotechnology, Alma Mater Studiorum","Istituto Italiano di Tecnologia","Universit\u00e0 di Bologna"],"raw_orcid":"https://orcid.org/0000-0003-2202-2000","affiliations":[{"raw_affiliation_string":"Computational and Chemical Biology","institution_ids":["https://openalex.org/I4210138427"]},{"raw_affiliation_string":"Department of Pharmacy and Biotechnology, Alma Mater Studiorum","institution_ids":["https://openalex.org/I2799787213"]},{"raw_affiliation_string":"Istituto Italiano di Tecnologia","institution_ids":["https://openalex.org/I30771326"]},{"raw_affiliation_string":"Universit\u00e0 di Bologna","institution_ids":["https://openalex.org/I9360294"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082187932","display_name":"Mattia Bernetti","orcid":"https://orcid.org/0000-0002-4373-9310"},"institutions":[{"id":"https://openalex.org/I1279970786","display_name":"Defense Information Systems Agency","ror":"https://ror.org/01xyx5098","country_code":"US","type":"government","lineage":["https://openalex.org/I1279970786","https://openalex.org/I1330347796"]},{"id":"https://openalex.org/I190397597","display_name":"University of Urbino","ror":"https://ror.org/04q4kt073","country_code":"IT","type":"education","lineage":["https://openalex.org/I190397597"]},{"id":"https://openalex.org/I30771326","display_name":"Italian Institute of Technology","ror":"https://ror.org/042t93s57","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326"]},{"id":"https://openalex.org/I4210138427","display_name":"Computational Physics (United States)","ror":"https://ror.org/03grsxg62","country_code":"US","type":"company","lineage":["https://openalex.org/I4210138427"]}],"countries":["IT","US"],"is_corresponding":true,"raw_author_name":"Mattia Bernetti","raw_affiliation_strings":["Computational and Chemical Biology","Department of Biomolecular Sciences (DISB)","Istituto Italiano di Tecnologia","Universit\u00e0 degli Studi di Urbino \u201cCarlo Bo\u201d"],"raw_orcid":"https://orcid.org/0000-0002-4373-9310","affiliations":[{"raw_affiliation_string":"Computational and Chemical Biology","institution_ids":["https://openalex.org/I4210138427"]},{"raw_affiliation_string":"Department of Biomolecular Sciences (DISB)","institution_ids":["https://openalex.org/I1279970786"]},{"raw_affiliation_string":"Istituto Italiano di Tecnologia","institution_ids":["https://openalex.org/I30771326"]},{"raw_affiliation_string":"Universit\u00e0 degli Studi di Urbino \u201cCarlo Bo\u201d","institution_ids":["https://openalex.org/I190397597"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024517861","display_name":"Gian Marco Elisi","orcid":"https://orcid.org/0000-0001-9071-5621"},"institutions":[{"id":"https://openalex.org/I1279970786","display_name":"Defense Information Systems Agency","ror":"https://ror.org/01xyx5098","country_code":"US","type":"government","lineage":["https://openalex.org/I1279970786","https://openalex.org/I1330347796"]},{"id":"https://openalex.org/I190397597","display_name":"University of Urbino","ror":"https://ror.org/04q4kt073","country_code":"IT","type":"education","lineage":["https://openalex.org/I190397597"]}],"countries":["IT","US"],"is_corresponding":false,"raw_author_name":"Gian Marco Elisi","raw_affiliation_strings":["Department of Biomolecular Sciences (DISB)","Universit\u00e0 degli Studi di Urbino \u201cCarlo Bo\u201d"],"raw_orcid":"https://orcid.org/0000-0001-9071-5621","affiliations":[{"raw_affiliation_string":"Department of Biomolecular Sciences (DISB)","institution_ids":["https://openalex.org/I1279970786"]},{"raw_affiliation_string":"Universit\u00e0 degli Studi di Urbino \u201cCarlo Bo\u201d","institution_ids":["https://openalex.org/I190397597"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5129940375","display_name":"Andrea Cavalli","orcid":null},"institutions":[{"id":"https://openalex.org/I2799787213","display_name":"Alma Mater Europaea","ror":"https://ror.org/028a67802","country_code":"SI","type":"education","lineage":["https://openalex.org/I2799787213"]},{"id":"https://openalex.org/I30771326","display_name":"Italian Institute of Technology","ror":"https://ror.org/042t93s57","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326"]},{"id":"https://openalex.org/I4210138427","display_name":"Computational Physics (United States)","ror":"https://ror.org/03grsxg62","country_code":"US","type":"company","lineage":["https://openalex.org/I4210138427"]},{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]},{"id":"https://openalex.org/I9360294","display_name":"University of Bologna","ror":"https://ror.org/01111rn36","country_code":"IT","type":"education","lineage":["https://openalex.org/I9360294"]}],"countries":["CH","IT","SI","US"],"is_corresponding":false,"raw_author_name":"Andrea Cavalli","raw_affiliation_strings":["Centre Europ\u00e9en de Calcul Atomique et Mol\u00e9culaire (CECAM)","Computational and Chemical Biology","Department of Pharmacy and Biotechnology, Alma Mater Studiorum","Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne","Istituto Italiano di Tecnologia","Universit\u00e0 di Bologna"],"raw_orcid":"https://orcid.org/0000-0002-6370-1176","affiliations":[{"raw_affiliation_string":"Centre Europ\u00e9en de Calcul Atomique et Mol\u00e9culaire (CECAM)","institution_ids":[]},{"raw_affiliation_string":"Computational and Chemical Biology","institution_ids":["https://openalex.org/I4210138427"]},{"raw_affiliation_string":"Department of Pharmacy and Biotechnology, Alma Mater Studiorum","institution_ids":["https://openalex.org/I2799787213"]},{"raw_affiliation_string":"Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne","institution_ids":["https://openalex.org/I5124864"]},{"raw_affiliation_string":"Istituto Italiano di Tecnologia","institution_ids":["https://openalex.org/I30771326"]},{"raw_affiliation_string":"Universit\u00e0 di Bologna","institution_ids":["https://openalex.org/I9360294"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5038881721","display_name":"Matteo Masetti","orcid":"https://orcid.org/0000-0002-3757-7802"},"institutions":[{"id":"https://openalex.org/I2799787213","display_name":"Alma Mater Europaea","ror":"https://ror.org/028a67802","country_code":"SI","type":"education","lineage":["https://openalex.org/I2799787213"]},{"id":"https://openalex.org/I9360294","display_name":"University of Bologna","ror":"https://ror.org/01111rn36","country_code":"IT","type":"education","lineage":["https://openalex.org/I9360294"]}],"countries":["IT","SI"],"is_corresponding":true,"raw_author_name":"Matteo Masetti","raw_affiliation_strings":["Department of Pharmacy and Biotechnology, Alma Mater Studiorum","Universit\u00e0 di Bologna"],"raw_orcid":"https://orcid.org/0000-0002-3757-7802","affiliations":[{"raw_affiliation_string":"Department of Pharmacy and Biotechnology, Alma Mater Studiorum","institution_ids":["https://openalex.org/I2799787213"]},{"raw_affiliation_string":"Universit\u00e0 di Bologna","institution_ids":["https://openalex.org/I9360294"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5038881721","https://openalex.org/A5082187932"],"corresponding_institution_ids":["https://openalex.org/I1279970786","https://openalex.org/I190397597","https://openalex.org/I2799787213","https://openalex.org/I30771326","https://openalex.org/I4210138427","https://openalex.org/I9360294"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.60015383,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"66","issue":"7","first_page":"4187","last_page":"4201"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.3287999927997589,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.3287999927997589,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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":0.1898999959230423,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.1842000037431717,"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":0.7935000061988831},{"id":"https://openalex.org/keywords/malat1","display_name":"MALAT1","score":0.474700003862381},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.4595000147819519},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.4542999863624573},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.4212999939918518},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.4185999929904938},{"id":"https://openalex.org/keywords/autodock","display_name":"AutoDock","score":0.3885999917984009},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.34790000319480896}],"concepts":[{"id":"https://openalex.org/C10679952","wikidata":"https://www.wikidata.org/wiki/Q5308937","display_name":"Druggability","level":3,"score":0.7935000061988831},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.7312999963760376},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.48089998960494995},{"id":"https://openalex.org/C2779134362","wikidata":"https://www.wikidata.org/wiki/Q18056223","display_name":"MALAT1","level":5,"score":0.474700003862381},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.4595000147819519},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4542999863624573},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.4212999939918518},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.4185999929904938},{"id":"https://openalex.org/C2780152424","wikidata":"https://www.wikidata.org/wiki/Q4826062","display_name":"AutoDock","level":4,"score":0.3885999917984009},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3668000102043152},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.34790000319480896},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.3285999894142151},{"id":"https://openalex.org/C68762167","wikidata":"https://www.wikidata.org/wiki/Q910164","display_name":"Cheminformatics","level":2,"score":0.31380000710487366},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.31209999322891235},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2985000014305115},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.29490000009536743},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.2865000069141388},{"id":"https://openalex.org/C41282012","wikidata":"https://www.wikidata.org/wiki/Q3928341","display_name":"RNA-binding protein","level":4,"score":0.2825999855995178},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.27810001373291016},{"id":"https://openalex.org/C2775937380","wikidata":"https://www.wikidata.org/wiki/Q1232589","display_name":"Replica","level":2,"score":0.2743000090122223},{"id":"https://openalex.org/C2989108626","wikidata":"https://www.wikidata.org/wiki/Q904407","display_name":"Drug target","level":2,"score":0.2574999928474426},{"id":"https://openalex.org/C70636015","wikidata":"https://www.wikidata.org/wiki/Q4300350","display_name":"Molecular biophysics","level":2,"score":0.2563999891281128}],"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":"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":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":true},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":true},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.5c02955","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c02955","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:41855101","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41855101","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":{"id":"doi:10.1021/acs.jcim.5c02955","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c02955","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":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.41679513454437256}],"awards":[{"id":"https://openalex.org/G1555660483","display_name":null,"funder_award_id":"J33C22001130001 CN00000041","funder_id":"https://openalex.org/F7311471023","funder_display_name":"NextGenerationEU"},{"id":"https://openalex.org/G4943812925","display_name":null,"funder_award_id":"J33C22001180001 CN00000013","funder_id":"https://openalex.org/F7311471023","funder_display_name":"NextGenerationEU"}],"funders":[{"id":"https://openalex.org/F7311471023","display_name":"NextGenerationEU","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":107,"referenced_works":["https://openalex.org/W1964789204","https://openalex.org/W1970741980","https://openalex.org/W1972758026","https://openalex.org/W1978967539","https://openalex.org/W1981225934","https://openalex.org/W1991794210","https://openalex.org/W2009463705","https://openalex.org/W2017835622","https://openalex.org/W2022597857","https://openalex.org/W2032183472","https://openalex.org/W2032741347","https://openalex.org/W2033094967","https://openalex.org/W2035687084","https://openalex.org/W2036402097","https://openalex.org/W2041638382","https://openalex.org/W2041652966","https://openalex.org/W2041882488","https://openalex.org/W2044444984","https://openalex.org/W2048792281","https://openalex.org/W2050273205","https://openalex.org/W2054191153","https://openalex.org/W2055891808","https://openalex.org/W2057477511","https://openalex.org/W2059013803","https://openalex.org/W2063622629","https://openalex.org/W2066690664","https://openalex.org/W2067174909","https://openalex.org/W2068205741","https://openalex.org/W2081046982","https://openalex.org/W2092915328","https://openalex.org/W2100561975","https://openalex.org/W2105349784","https://openalex.org/W2105668062","https://openalex.org/W2110957978","https://openalex.org/W2116168949","https://openalex.org/W2122774834","https://openalex.org/W2128572087","https://openalex.org/W2128619556","https://openalex.org/W2129375421","https://openalex.org/W2135302954","https://openalex.org/W2136729627","https://openalex.org/W2141172277","https://openalex.org/W2144288821","https://openalex.org/W2164846849","https://openalex.org/W2216341974","https://openalex.org/W2259938310","https://openalex.org/W2271736303","https://openalex.org/W2396723088","https://openalex.org/W2744078451","https://openalex.org/W2747089052","https://openalex.org/W2751498235","https://openalex.org/W2753719005","https://openalex.org/W2770371168","https://openalex.org/W2782369838","https://openalex.org/W2783337342","https://openalex.org/W2791338205","https://openalex.org/W2794774007","https://openalex.org/W2806353550","https://openalex.org/W2820941669","https://openalex.org/W2885145257","https://openalex.org/W2887889028","https://openalex.org/W2888364023","https://openalex.org/W2897570487","https://openalex.org/W2901082097","https://openalex.org/W2903139824","https://openalex.org/W2910703604","https://openalex.org/W2921713582","https://openalex.org/W2943588752","https://openalex.org/W2974711963","https://openalex.org/W3035076119","https://openalex.org/W3120361527","https://openalex.org/W3127634170","https://openalex.org/W3146626743","https://openalex.org/W3167019654","https://openalex.org/W3168436232","https://openalex.org/W3174373983","https://openalex.org/W4231404431","https://openalex.org/W4281760545","https://openalex.org/W4285331314","https://openalex.org/W4292348647","https://openalex.org/W4292651781","https://openalex.org/W4309012911","https://openalex.org/W4321765962","https://openalex.org/W4366819686","https://openalex.org/W4380422613","https://openalex.org/W4384625873","https://openalex.org/W4385073511","https://openalex.org/W4385331434","https://openalex.org/W4388719212","https://openalex.org/W4392962601","https://openalex.org/W4396237136","https://openalex.org/W4399049435","https://openalex.org/W4400777964","https://openalex.org/W4401584128","https://openalex.org/W4401633750","https://openalex.org/W4401633979","https://openalex.org/W4402307067","https://openalex.org/W4404083867","https://openalex.org/W4405570896","https://openalex.org/W4406629486","https://openalex.org/W4406970630","https://openalex.org/W4407323036","https://openalex.org/W4409683253","https://openalex.org/W4411077643","https://openalex.org/W4411783921","https://openalex.org/W4412110792","https://openalex.org/W4414702422"],"related_works":[],"abstract_inverted_index":{"Long":[0],"noncoding":[1],"RNAs":[2],"(lncRNAs)":[3],"are":[4],"increasingly":[5],"recognized":[6],"as":[7],"druggable":[8],"targets":[9,160],"due":[10],"to":[11,63,114,139],"their":[12],"conserved":[13],"secondary/tertiary":[14],"structures":[15],"and":[16,34,59,83,98,109,151,161],"regulatory":[17],"roles":[18],"in":[19,37,168],"disease.":[20],"A":[21],"prototypical":[22],"example":[23],"is":[24,35],"the":[25,42,65,115,122,126,141,149],"MALAT1":[26],"triple":[27],"helix,":[28],"whose":[29],"stability":[30],"supports":[31],"transcript":[32],"persistence":[33],"implicated":[36],"oncogenesis.":[38],"Here,":[39],"we":[40],"evaluate":[41],"ability":[43],"of":[44,68,117,131,153],"a":[45,118,163],"structure-based":[46],"drug":[47,170],"discovery":[48],"(SBDD)":[49],"pipeline,":[50],"integrating":[51],"molecular":[52],"dynamics":[53],"(MD),":[54],"pocket":[55],"analysis,":[56],"ensemble":[57],"docking,":[58],"diverse":[60],"scoring":[61,111],"functions,":[62,112],"capture":[64],"binding":[66,91,119],"behavior":[67],"21":[69],"congeneric":[70],"diminazene-based":[71],"ligands":[72],"targeting":[73],"MALAT1.":[74],"Conformational":[75],"ensembles":[76],"were":[77],"generated":[78],"using":[79],"both":[80],"conventional":[81],"MD":[82],"Hamiltonian":[84],"Replica":[85],"Exchange":[86],"MD,":[87],"revealing":[88],"two":[89],"potential":[90],"sites.":[92],"Ensemble":[93],"docking":[94],"with":[95,107,121],"AutoDock":[96],"GPU":[97],"rDock":[99],"across":[100,125],"representative":[101],"RNA":[102,159],"conformations,":[103],"followed":[104],"by":[105],"rescoring":[106],"force-field":[108],"machine-learning-based":[110],"led":[113],"identification":[116],"mode":[120],"best":[123],"agreement":[124],"series.":[127],"Principal":[128],"component":[129],"analysis":[130],"interaction":[132],"fingerprints":[133],"within":[134],"clustered":[135],"poses":[136],"was":[137],"used":[138],"explain":[140],"experimentally":[142],"observed":[143],"affinity":[144],"trends.":[145],"Our":[146],"findings":[147],"highlight":[148],"promise":[150],"limitations":[152],"current":[154],"SBDD":[155],"pipelines":[156],"for":[157,165],"flexible":[158],"offer":[162],"benchmark":[164],"future":[166],"improvement":[167],"RNA-focused":[169],"discovery.":[171]},"counts_by_year":[],"updated_date":"2026-04-14T06:02:45.956762","created_date":"2026-03-20T00:00:00"}
