{"id":"https://openalex.org/W2169811655","doi":"https://doi.org/10.1186/s12859-015-0718-6","title":"New in silico approach to assessing RNA secondary structures with non-canonical base pairs","display_name":"New in silico approach to assessing RNA secondary structures with non-canonical base pairs","publication_year":2015,"publication_date":"2015-09-01","ids":{"openalex":"https://openalex.org/W2169811655","doi":"https://doi.org/10.1186/s12859-015-0718-6","mag":"2169811655","pmid":"https://pubmed.ncbi.nlm.nih.gov/26329823"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-015-0718-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0718-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0718-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0718-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027621077","display_name":"Agnieszka Rybarczyk","orcid":"https://orcid.org/0000-0003-4115-0737"},"institutions":[{"id":"https://openalex.org/I4210152414","display_name":"Institute of Bioorganic Chemistry, Polish Academy of Sciences","ror":"https://ror.org/04ejdtr48","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210152414","https://openalex.org/I99542240"]},{"id":"https://openalex.org/I46597724","display_name":"Pozna\u0144 University of Technology","ror":"https://ror.org/00p7p3302","country_code":"PL","type":"education","lineage":["https://openalex.org/I46597724"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Agnieszka Rybarczyk","raw_affiliation_strings":["Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland. arybarczyk@cs.put.poznan.pl","Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland. arybarczyk@cs.put.poznan.pl","Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland. arybarczyk@cs.put.poznan.pl","institution_ids":["https://openalex.org/I4210152414"]},{"raw_affiliation_string":"Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland. arybarczyk@cs.put.poznan.pl","institution_ids":["https://openalex.org/I46597724"]},{"raw_affiliation_string":"Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland","institution_ids":["https://openalex.org/I46597724"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051618054","display_name":"Natalia Sz\u00f3stak","orcid":"https://orcid.org/0000-0001-9933-0496"},"institutions":[{"id":"https://openalex.org/I46597724","display_name":"Pozna\u0144 University of Technology","ror":"https://ror.org/00p7p3302","country_code":"PL","type":"education","lineage":["https://openalex.org/I46597724"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Natalia Szostak","raw_affiliation_strings":["Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland. nszostak@cs.put.poznan.pl","Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland. nszostak@cs.put.poznan.pl","institution_ids":["https://openalex.org/I46597724"]},{"raw_affiliation_string":"Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland","institution_ids":["https://openalex.org/I46597724"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045163807","display_name":"Maciej Antczak","orcid":"https://orcid.org/0000-0002-5320-2023"},"institutions":[{"id":"https://openalex.org/I46597724","display_name":"Pozna\u0144 University of Technology","ror":"https://ror.org/00p7p3302","country_code":"PL","type":"education","lineage":["https://openalex.org/I46597724"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Maciej Antczak","raw_affiliation_strings":["Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland. mantczak@cs.put.poznan.pl","Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland. mantczak@cs.put.poznan.pl","institution_ids":["https://openalex.org/I46597724"]},{"raw_affiliation_string":"Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland","institution_ids":["https://openalex.org/I46597724"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091783406","display_name":"Tomasz \u017bok","orcid":"https://orcid.org/0000-0003-4103-9238"},"institutions":[{"id":"https://openalex.org/I46597724","display_name":"Pozna\u0144 University of Technology","ror":"https://ror.org/00p7p3302","country_code":"PL","type":"education","lineage":["https://openalex.org/I46597724"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Tomasz Zok","raw_affiliation_strings":["Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland. tzok@cs.put.poznan.pl","Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland. tzok@cs.put.poznan.pl","institution_ids":["https://openalex.org/I46597724"]},{"raw_affiliation_string":"Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland","institution_ids":["https://openalex.org/I46597724"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018487426","display_name":"Mariusz Popenda","orcid":"https://orcid.org/0000-0001-9965-0430"},"institutions":[{"id":"https://openalex.org/I4210152414","display_name":"Institute of Bioorganic Chemistry, Polish Academy of Sciences","ror":"https://ror.org/04ejdtr48","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210152414","https://openalex.org/I99542240"]},{"id":"https://openalex.org/I46597724","display_name":"Pozna\u0144 University of Technology","ror":"https://ror.org/00p7p3302","country_code":"PL","type":"education","lineage":["https://openalex.org/I46597724"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Mariusz Popenda","raw_affiliation_strings":["European Center for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland. mariusz.popenda@ibch.poznan.pl","Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland. mariusz.popenda@ibch.poznan.pl","Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Center for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland. mariusz.popenda@ibch.poznan.pl","institution_ids":["https://openalex.org/I46597724"]},{"raw_affiliation_string":"Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland. mariusz.popenda@ibch.poznan.pl","institution_ids":["https://openalex.org/I4210152414"]},{"raw_affiliation_string":"Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland","institution_ids":["https://openalex.org/I4210152414"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066355029","display_name":"Ryszard W. Adamiak","orcid":"https://orcid.org/0000-0001-8914-9618"},"institutions":[{"id":"https://openalex.org/I4210152414","display_name":"Institute of Bioorganic Chemistry, Polish Academy of Sciences","ror":"https://ror.org/04ejdtr48","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210152414","https://openalex.org/I99542240"]},{"id":"https://openalex.org/I46597724","display_name":"Pozna\u0144 University of Technology","ror":"https://ror.org/00p7p3302","country_code":"PL","type":"education","lineage":["https://openalex.org/I46597724"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Ryszard Adamiak","raw_affiliation_strings":["European Center for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland. ryszard.adamiak@ibch.poznan.pl","Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland. ryszard.adamiak@ibch.poznan.pl","Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Center for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland. ryszard.adamiak@ibch.poznan.pl","institution_ids":["https://openalex.org/I46597724"]},{"raw_affiliation_string":"Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland. ryszard.adamiak@ibch.poznan.pl","institution_ids":["https://openalex.org/I4210152414"]},{"raw_affiliation_string":"Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland","institution_ids":["https://openalex.org/I4210152414"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024504556","display_name":"Jacek B\u0142a\u017cewicz","orcid":"https://orcid.org/0000-0001-8326-1094"},"institutions":[{"id":"https://openalex.org/I4210152414","display_name":"Institute of Bioorganic Chemistry, Polish Academy of Sciences","ror":"https://ror.org/04ejdtr48","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210152414","https://openalex.org/I99542240"]},{"id":"https://openalex.org/I46597724","display_name":"Pozna\u0144 University of Technology","ror":"https://ror.org/00p7p3302","country_code":"PL","type":"education","lineage":["https://openalex.org/I46597724"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Jacek Blazewicz","raw_affiliation_strings":["Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland. jblazewicz@cs.put.poznan.pl","Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland. jblazewicz@cs.put.poznan.pl","Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland. jblazewicz@cs.put.poznan.pl","institution_ids":["https://openalex.org/I4210152414"]},{"raw_affiliation_string":"Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland. jblazewicz@cs.put.poznan.pl","institution_ids":["https://openalex.org/I46597724"]},{"raw_affiliation_string":"Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland","institution_ids":["https://openalex.org/I46597724"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056736610","display_name":"Marta Szachniuk","orcid":"https://orcid.org/0000-0002-8724-7908"},"institutions":[{"id":"https://openalex.org/I4210152414","display_name":"Institute of Bioorganic Chemistry, Polish Academy of Sciences","ror":"https://ror.org/04ejdtr48","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210152414","https://openalex.org/I99542240"]},{"id":"https://openalex.org/I46597724","display_name":"Pozna\u0144 University of Technology","ror":"https://ror.org/00p7p3302","country_code":"PL","type":"education","lineage":["https://openalex.org/I46597724"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Marta Szachniuk","raw_affiliation_strings":["Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland. mszachniuk@cs.put.poznan.pl","Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland. mszachniuk@cs.put.poznan.pl","Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland. mszachniuk@cs.put.poznan.pl","institution_ids":["https://openalex.org/I4210152414"]},{"raw_affiliation_string":"Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland. mszachniuk@cs.put.poznan.pl","institution_ids":["https://openalex.org/I46597724"]},{"raw_affiliation_string":"Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland","institution_ids":["https://openalex.org/I4210152414"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5056736610"],"corresponding_institution_ids":["https://openalex.org/I4210152414","https://openalex.org/I46597724"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":1.9281,"has_fulltext":true,"cited_by_count":37,"citation_normalized_percentile":{"value":0.86188535,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"16","issue":"1","first_page":"276","last_page":"276"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9616000056266785,"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":0.9616000056266785,"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/T11162","display_name":"Enzyme Structure and Function","score":0.005200000014156103,"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/T11445","display_name":"Origins and Evolution of Life","score":0.00419999985024333,"subfield":{"id":"https://openalex.org/subfields/3103","display_name":"Astronomy and Astrophysics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.7403285503387451},{"id":"https://openalex.org/keywords/protein-secondary-structure","display_name":"Protein secondary structure","score":0.6864784359931946},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.6243487596511841},{"id":"https://openalex.org/keywords/pseudoknot","display_name":"Pseudoknot","score":0.6150521636009216},{"id":"https://openalex.org/keywords/base-pair","display_name":"Base pair","score":0.580341100692749},{"id":"https://openalex.org/keywords/nucleic-acid-structure","display_name":"Nucleic acid structure","score":0.5501858592033386},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5326117277145386},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5157387852668762},{"id":"https://openalex.org/keywords/wobble-base-pair","display_name":"Wobble base pair","score":0.4476708769798279},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.4212116599082947},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.42086061835289},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3516030013561249},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3314248323440552},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32740217447280884},{"id":"https://openalex.org/keywords/transfer-rna","display_name":"Transfer RNA","score":0.27415966987609863},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2265133559703827},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21162134408950806},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07637479901313782}],"concepts":[{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.7403285503387451},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.6864784359931946},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.6243487596511841},{"id":"https://openalex.org/C105130999","wikidata":"https://www.wikidata.org/wiki/Q414976","display_name":"Pseudoknot","level":4,"score":0.6150521636009216},{"id":"https://openalex.org/C185581394","wikidata":"https://www.wikidata.org/wiki/Q145911","display_name":"Base pair","level":3,"score":0.580341100692749},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.5501858592033386},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5326117277145386},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5157387852668762},{"id":"https://openalex.org/C203353237","wikidata":"https://www.wikidata.org/wiki/Q2141556","display_name":"Wobble base pair","level":5,"score":0.4476708769798279},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.4212116599082947},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.42086061835289},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3516030013561249},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3314248323440552},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32740217447280884},{"id":"https://openalex.org/C153957851","wikidata":"https://www.wikidata.org/wiki/Q201448","display_name":"Transfer RNA","level":4,"score":0.27415966987609863},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2265133559703827},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21162134408950806},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07637479901313782},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1186/s12859-015-0718-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0718-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0718-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26329823","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26329823","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:3535832","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4557229","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-015-0718-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0718-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0718-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2344598488","display_name":null,"funder_award_id":"2012/06/A/ST6/00384","funder_id":"https://openalex.org/F4320322511","funder_display_name":"Narodowe Centrum Nauki"},{"id":"https://openalex.org/G6034578193","display_name":null,"funder_award_id":"2012/05/B/ST6/03026","funder_id":"https://openalex.org/F4320322511","funder_display_name":"Narodowe Centrum Nauki"}],"funders":[{"id":"https://openalex.org/F4320310077","display_name":"National Research Centre","ror":"https://ror.org/02n85j827"},{"id":"https://openalex.org/F4320322511","display_name":"Narodowe Centrum Nauki","ror":"https://ror.org/03ha2q922"},{"id":"https://openalex.org/F4320322733","display_name":"Ministerstwo Edukacji i Nauki","ror":"https://ror.org/05dwvd537"},{"id":"https://openalex.org/F4320335327","display_name":"Krajowy Naukowy Osrodek Wiodacy","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2169811655.pdf","grobid_xml":"https://content.openalex.org/works/W2169811655.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W280694366","https://openalex.org/W577926080","https://openalex.org/W1543796220","https://openalex.org/W1584476217","https://openalex.org/W1971767242","https://openalex.org/W1980722147","https://openalex.org/W1984882637","https://openalex.org/W1988409793","https://openalex.org/W2000074786","https://openalex.org/W2003122343","https://openalex.org/W2023013439","https://openalex.org/W2053150979","https://openalex.org/W2059099058","https://openalex.org/W2061539493","https://openalex.org/W2077064224","https://openalex.org/W2091705944","https://openalex.org/W2098571862","https://openalex.org/W2102017611","https://openalex.org/W2103848900","https://openalex.org/W2106478835","https://openalex.org/W2106595865","https://openalex.org/W2115660112","https://openalex.org/W2115729502","https://openalex.org/W2118780761","https://openalex.org/W2119896557","https://openalex.org/W2122774834","https://openalex.org/W2125126793","https://openalex.org/W2133279885","https://openalex.org/W2141494692","https://openalex.org/W2143407915","https://openalex.org/W2150404344","https://openalex.org/W2158073100","https://openalex.org/W2162078089","https://openalex.org/W2162224067","https://openalex.org/W2167564948","https://openalex.org/W2170441710","https://openalex.org/W3104468196","https://openalex.org/W6616862856"],"related_works":["https://openalex.org/W1966171024","https://openalex.org/W2148725278","https://openalex.org/W2159621058","https://openalex.org/W4225160382","https://openalex.org/W2954092143","https://openalex.org/W1583489351","https://openalex.org/W1999060916","https://openalex.org/W2141351700","https://openalex.org/W2135373808","https://openalex.org/W1997175692"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,61,208,223],"function":[2,51],"of":[3,15,21,24,33,43,49,99,107,184],"RNA":[4,50,62,108,124,146,199,216,245],"is":[5,23,30,110,141],"strongly":[6],"dependent":[7],"on":[8,18,57,143],"its":[9],"structure,":[10,17,40,109,126],"so":[11],"an":[12,47,122],"appropriate":[13],"recognition":[14],"this":[16,177],"every":[19],"level":[20],"organization,":[22],"great":[25],"importance.":[26],"One":[27],"particular":[28],"concern":[29],"the":[31,38,41,58,145,166,182,197,239],"assessment":[32,237],"base-base":[34],"interactions,":[35,101],"described":[36],"as":[37],"secondary":[39,63,125,155,168,246],"knowledge":[42],"which":[44,127],"greatly":[45],"facilitates":[46],"interpretation":[48],"and":[52,94,131,163,202,220,228],"allows":[53],"for":[54,103,196,204,215],"structure":[55,64,84,148,156,169,200,218],"analysis":[56],"tertiary":[59],"level.":[60],"can":[65],"be":[66],"predicted":[67],"from":[68,82,149,170],"a":[69,104,150,154,192],"sequence":[70,152],"using":[71],"in":[72,191,233],"silico":[73],"methods":[74,190,241],"often":[75],"adjusted":[76],"with":[77,136],"experimental":[78],"data,":[79],"or":[80,153],"assessed":[81],"3D":[83,147,198,217],"atom":[85,171],"coordinates.":[86,172],"Computational":[87],"approaches":[88],"typically":[89],"consider":[90],"only":[91,158],"canonical,":[92],"Watson-Crick":[93],"wobble":[95],"base":[96,133,161,235],"pairs.":[97],"Handling":[98],"non-canonical":[100,132,234],"important":[102],"full":[105],"description":[106],"still":[111],"very":[112],"difficult.":[113],"RESULTS:":[114],"We":[115],"introduce":[116],"our":[117,174],"novel":[118],"approach":[119],"to":[120],"assessing":[121],"extended":[123,167],"characterizes":[128],"both":[129],"canonical":[130,160],"pairs,":[134,162],"along":[135],"their":[137],"type":[138],"classification.":[139],"It":[140],"based":[142],"predicting":[144],"user-provided":[151],"that":[157,242],"describes":[159],"then":[164],"deriving":[165],"In":[173],"example":[175,224],"implementation,":[176],"was":[178],"achieved":[179],"by":[180],"integrating":[181],"functionality":[183],"two":[185],"fully":[186],"automated,":[187],"high":[188],"fidelity":[189],"computational":[193],"pipeline:":[194],"RNAComposer":[195,227],"prediction":[201,219],"RNApdbee":[203],"base-pair":[205,221],"annotation.":[206,222],"CONCLUSIONS:":[207],"presented":[209],"methodology":[210],"ties":[211],"together":[212],"existing":[213],"applications":[214],"performance,":[225],"applying":[226],"RNApdbee,":[229],"reveals":[230],"better":[231],"accuracy":[232],"pair":[236],"than":[238],"compared":[240],"directly":[243],"predict":[244],"structure.":[247]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":5}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
