{"id":"https://openalex.org/W4281760545","doi":"https://doi.org/10.1371/journal.pcbi.1009783","title":"fingeRNAt\u2014A novel tool for high-throughput analysis of nucleic acid-ligand interactions","display_name":"fingeRNAt\u2014A novel tool for high-throughput analysis of nucleic acid-ligand interactions","publication_year":2022,"publication_date":"2022-06-02","ids":{"openalex":"https://openalex.org/W4281760545","doi":"https://doi.org/10.1371/journal.pcbi.1009783","pmid":"https://pubmed.ncbi.nlm.nih.gov/35653385"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1009783","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009783","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009783&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009783&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064645044","display_name":"Natalia A. Szulc","orcid":"https://orcid.org/0000-0002-2991-3634"},"institutions":[{"id":"https://openalex.org/I4210120699","display_name":"International Institute of Molecular and Cell Biology","ror":"https://ror.org/01y3dkx74","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210120699"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Natalia A. Szulc","raw_affiliation_strings":["Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland"],"raw_orcid":"https://orcid.org/0000-0002-2991-3634","affiliations":[{"raw_affiliation_string":"Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland","institution_ids":["https://openalex.org/I4210120699"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047068703","display_name":"Zuzanna Mackiewicz","orcid":"https://orcid.org/0000-0003-1654-9025"},"institutions":[{"id":"https://openalex.org/I4210120699","display_name":"International Institute of Molecular and Cell Biology","ror":"https://ror.org/01y3dkx74","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210120699"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Zuzanna Mackiewicz","raw_affiliation_strings":["Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland"],"raw_orcid":"https://orcid.org/0000-0003-1654-9025","affiliations":[{"raw_affiliation_string":"Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland","institution_ids":["https://openalex.org/I4210120699"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003280938","display_name":"Janusz M. Bujnicki","orcid":"https://orcid.org/0000-0002-6633-165X"},"institutions":[{"id":"https://openalex.org/I4210120699","display_name":"International Institute of Molecular and Cell Biology","ror":"https://ror.org/01y3dkx74","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210120699"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Janusz M. Bujnicki","raw_affiliation_strings":["Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland"],"raw_orcid":"https://orcid.org/0000-0002-6633-165X","affiliations":[{"raw_affiliation_string":"Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland","institution_ids":["https://openalex.org/I4210120699"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021047504","display_name":"Filip Stefaniak","orcid":"https://orcid.org/0000-0001-5758-9416"},"institutions":[{"id":"https://openalex.org/I4210120699","display_name":"International Institute of Molecular and Cell Biology","ror":"https://ror.org/01y3dkx74","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210120699"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Filip Stefaniak","raw_affiliation_strings":["Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland"],"raw_orcid":"https://orcid.org/0000-0001-5758-9416","affiliations":[{"raw_affiliation_string":"Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland","institution_ids":["https://openalex.org/I4210120699"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5003280938","https://openalex.org/A5021047504","https://openalex.org/A5064645044"],"corresponding_institution_ids":["https://openalex.org/I4210120699"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.9963,"has_fulltext":true,"cited_by_count":25,"citation_normalized_percentile":{"value":0.8695018,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"18","issue":"6","first_page":"e1009783","last_page":"e1009783"},"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/T10604","display_name":"RNA Research and Splicing","score":0.9990000128746033,"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/T11482","display_name":"RNA modifications and cancer","score":0.9987000226974487,"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/nucleic-acid","display_name":"Nucleic acid","score":0.6026403903961182},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5746217966079712},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.5499571561813354},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4014240503311157},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3584517538547516},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2668308913707733},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.2246258556842804}],"concepts":[{"id":"https://openalex.org/C24107716","wikidata":"https://www.wikidata.org/wiki/Q123619","display_name":"Nucleic acid","level":2,"score":0.6026403903961182},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5746217966079712},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.5499571561813354},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4014240503311157},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3584517538547516},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2668308913707733},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2246258556842804},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.0},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0}],"mesh":[{"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":"D009696","descriptor_name":"Nucleic Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009696","descriptor_name":"Nucleic Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009696","descriptor_name":"Nucleic Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1009783","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009783","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009783&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:35653385","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35653385","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:6cbd49b2c37344c7a5bbee1e99d33373","is_oa":true,"landing_page_url":"https://doaj.org/article/6cbd49b2c37344c7a5bbee1e99d33373","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":"PLoS Computational Biology, Vol 18, Iss 6, p e1009783 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9197077","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9197077","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":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1009783","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009783","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009783&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1866387804","display_name":null,"funder_award_id":"POIR.04.04.00-00-3CF0/16","funder_id":"https://openalex.org/F4320321042","funder_display_name":"Fundacja na rzecz Nauki Polskiej"},{"id":"https://openalex.org/G2055366924","display_name":null,"funder_award_id":"2020/39/B/NZ2/03127","funder_id":"https://openalex.org/F4320322511","funder_display_name":"Narodowe Centrum Nauki"},{"id":"https://openalex.org/G3487719301","display_name":null,"funder_award_id":"POIR.04.04.00-00-3CF0/16","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"}],"funders":[{"id":"https://openalex.org/F4320321042","display_name":"Fundacja na rzecz Nauki Polskiej","ror":"https://ror.org/048zd9m77"},{"id":"https://openalex.org/F4320322511","display_name":"Narodowe Centrum Nauki","ror":"https://ror.org/03ha2q922"},{"id":"https://openalex.org/F4320322650","display_name":"Narodowym Centrum Nauki","ror":"https://ror.org/03ha2q922"},{"id":"https://openalex.org/F4320323873","display_name":"Uniwersytet Warszawski","ror":"https://ror.org/039bjqg32"},{"id":"https://openalex.org/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4281760545.pdf"},"referenced_works_count":134,"referenced_works":["https://openalex.org/W625272620","https://openalex.org/W1531524766","https://openalex.org/W1586243412","https://openalex.org/W1703081596","https://openalex.org/W1835740130","https://openalex.org/W1968319881","https://openalex.org/W1974158203","https://openalex.org/W1980022131","https://openalex.org/W1980337077","https://openalex.org/W1985748743","https://openalex.org/W1988286515","https://openalex.org/W1992947643","https://openalex.org/W1993319845","https://openalex.org/W1993961204","https://openalex.org/W1994195216","https://openalex.org/W1995952752","https://openalex.org/W1998410234","https://openalex.org/W1999474945","https://openalex.org/W2002433816","https://openalex.org/W2009349503","https://openalex.org/W2014430663","https://openalex.org/W2015647379","https://openalex.org/W2018841730","https://openalex.org/W2019875938","https://openalex.org/W2023638011","https://openalex.org/W2025816743","https://openalex.org/W2026395206","https://openalex.org/W2028649050","https://openalex.org/W2032456809","https://openalex.org/W2036150293","https://openalex.org/W2038138598","https://openalex.org/W2041877730","https://openalex.org/W2042629681","https://openalex.org/W2043509228","https://openalex.org/W2044444984","https://openalex.org/W2046792302","https://openalex.org/W2048792281","https://openalex.org/W2051907189","https://openalex.org/W2052818547","https://openalex.org/W2053503396","https://openalex.org/W2054525948","https://openalex.org/W2062781904","https://openalex.org/W2069737052","https://openalex.org/W2071555876","https://openalex.org/W2074374189","https://openalex.org/W2074473216","https://openalex.org/W2076790509","https://openalex.org/W2078334480","https://openalex.org/W2081912151","https://openalex.org/W2084014179","https://openalex.org/W2086004174","https://openalex.org/W2086402273","https://openalex.org/W2088423689","https://openalex.org/W2089447985","https://openalex.org/W2092915328","https://openalex.org/W2098631451","https://openalex.org/W2098735395","https://openalex.org/W2100598991","https://openalex.org/W2100757581","https://openalex.org/W2101234009","https://openalex.org/W2106466007","https://openalex.org/W2110283222","https://openalex.org/W2114326383","https://openalex.org/W2119896557","https://openalex.org/W2129726167","https://openalex.org/W2130025410","https://openalex.org/W2130359029","https://openalex.org/W2132629607","https://openalex.org/W2132976721","https://openalex.org/W2133742529","https://openalex.org/W2143482176","https://openalex.org/W2151697120","https://openalex.org/W2151957804","https://openalex.org/W2152040212","https://openalex.org/W2153641594","https://openalex.org/W2161636168","https://openalex.org/W2162477138","https://openalex.org/W2163639779","https://openalex.org/W2165759309","https://openalex.org/W2166344128","https://openalex.org/W2166668953","https://openalex.org/W2168045053","https://openalex.org/W2169615567","https://openalex.org/W2169678694","https://openalex.org/W2238068487","https://openalex.org/W2283777186","https://openalex.org/W2314179822","https://openalex.org/W2317406936","https://openalex.org/W2395425574","https://openalex.org/W2442594675","https://openalex.org/W2494433368","https://openalex.org/W2502698579","https://openalex.org/W2517268481","https://openalex.org/W2549659896","https://openalex.org/W2560264526","https://openalex.org/W2598816856","https://openalex.org/W2605573491","https://openalex.org/W2612329522","https://openalex.org/W2659331658","https://openalex.org/W2739354641","https://openalex.org/W2794940806","https://openalex.org/W2820941669","https://openalex.org/W2889677957","https://openalex.org/W2895061638","https://openalex.org/W2921693553","https://openalex.org/W2951804018","https://openalex.org/W2955998834","https://openalex.org/W2958873833","https://openalex.org/W2980233439","https://openalex.org/W2985871121","https://openalex.org/W2992752586","https://openalex.org/W2999636761","https://openalex.org/W3003257820","https://openalex.org/W3015273333","https://openalex.org/W3022554208","https://openalex.org/W3023794997","https://openalex.org/W3027546635","https://openalex.org/W3034073642","https://openalex.org/W3044901108","https://openalex.org/W3082990758","https://openalex.org/W3084513853","https://openalex.org/W3103145119","https://openalex.org/W3127634170","https://openalex.org/W3129321183","https://openalex.org/W3132447912","https://openalex.org/W3157078379","https://openalex.org/W3159177617","https://openalex.org/W3163201454","https://openalex.org/W3171835979","https://openalex.org/W3192540610","https://openalex.org/W3203735717","https://openalex.org/W4250690753","https://openalex.org/W6638693577","https://openalex.org/W6675354045"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2899084033","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W4391375266","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W1976181487"],"abstract_inverted_index":{"Computational":[0],"methods":[1],"play":[2],"a":[3,139,170,190],"pivotal":[4],"role":[5],"in":[6,13,30,48,91,182,202,234,242],"drug":[7,67],"discovery":[8],"and":[9,18,39,56,107,124,167,195,223,293],"are":[10,164],"widely":[11],"applied":[12],"virtual":[14],"screening,":[15],"structure":[16],"optimization,":[17],"compound":[19],"activity":[20],"profiling.":[21],"Over":[22],"the":[23,28,70,129,151,157,179,183,243,275],"last":[24],"decades,":[25],"almost":[26],"all":[27],"attention":[29,64],"medicinal":[31],"chemistry":[32],"has":[33],"been":[34,43],"directed":[35],"to":[36,187,196,256,258,285],"protein-ligand":[37],"binding,":[38],"computational":[40,224],"tools":[41,74],"have":[42,61,295],"created":[44],"with":[45,96,261],"this":[46],"target":[47],"mind.":[49],"With":[50],"novel":[51],"discoveries":[52],"of":[53,72,93,103,131,159,207,217,226,231,271,277],"functional":[54],"RNAs":[55,60],"their":[57],"possible":[58],"applications,":[59],"gained":[62],"considerable":[63],"as":[65,169,252],"potential":[66],"targets.":[68],"However,":[69,128],"availability":[71],"bioinformatics":[73],"for":[75,86,221,274],"nucleic":[76,94],"acids":[77,95],"is":[78,185,193,302],"limited.":[79],"Here,":[80],"we":[81],"introduce":[82],"fingeRNAt-a":[83],"software":[84,301],"tool":[85],"detecting":[87],"non-covalent":[88],"interactions":[89,133,146,232,263],"formed":[90,233],"complexes":[92,240,260],"ligands.":[97],"The":[98,299],"program":[99],"detects":[100],"nine":[101],"types":[102],"interactions:":[104],"(i)":[105],"hydrogen":[106],"(ii)":[108],"halogen":[109],"bonds,":[110],"(iii)":[111],"cation-anion,":[112],"(iv)":[113],"pi-cation,":[114],"(v)":[115],"pi-anion,":[116],"(vi)":[117],"pi-stacking,":[118],"(vii)":[119],"inorganic":[120],"ion-mediated,":[121],"(viii)":[122],"water-mediated,":[123],"(ix)":[125],"lipophilic":[126],"interactions.":[127],"scope":[130],"detected":[132,145],"can":[134,147,282],"be":[135,148,283],"easily":[136],"expanded":[137],"using":[138,150,210],"simple":[140],"plugin":[141],"system.":[142],"In":[143],"addition,":[144],"visualized":[149],"associated":[152],"PyMOL":[153],"plugin,":[154],"which":[155],"facilitates":[156],"analysis":[158,206,212,225,230],"medium-throughput":[160],"molecular":[161,278],"complexes.":[162,279],"Interactions":[163],"also":[165],"encoded":[166],"stored":[168],"bioinformatics-friendly":[171],"Structural":[172],"Interaction":[173],"Fingerprint":[174],"(SIFt)-a":[175],"binary":[176],"string":[177],"where":[178],"respective":[180],"bit":[181],"fingerprint":[184],"set":[186],"1":[188],"if":[189],"particular":[191],"interaction":[192,208,219,249,272],"present":[194,215,268],"0":[197],"otherwise.":[198],"This":[199,280],"output":[200],"format,":[201],"turn,":[203],"enables":[204],"high-throughput":[205],"data":[209,211],"techniques.":[213],"We":[214,247,267],"applications":[216],"fingeRNAt-generated":[218],"fingerprints":[220,273],"visual":[222],"RNA-ligand":[227],"complexes,":[228],"including":[229],"experimentally":[235],"determined":[236],"RNA-small":[237],"molecule":[238],"ligand":[239],"deposited":[241],"Protein":[244],"Data":[245],"Bank.":[246],"propose":[248],"fingerprint-based":[250],"similarity":[251],"an":[253,269],"alternative":[254],"measure":[255],"RMSD":[257],"recapitulate":[259],"similar":[262,290,296],"but":[264],"different":[265],"folding.":[266],"application":[270],"clustering":[276],"approach":[281],"used":[284],"group":[286],"ligands":[287],"that":[288],"form":[289],"binding":[291],"networks":[292],"thus":[294],"biological":[297],"properties.":[298],"fingeRNAt":[300],"freely":[303],"available":[304],"at":[305],"https://github.com/n-szulc/fingeRNAt.":[306]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":2}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
