{"id":"https://openalex.org/W2133182629","doi":"https://doi.org/10.1093/nar/gks412","title":"Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming","display_name":"Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming","publication_year":2012,"publication_date":"2012-05-16","ids":{"openalex":"https://openalex.org/W2133182629","doi":"https://doi.org/10.1093/nar/gks412","mag":"2133182629","pmid":"https://pubmed.ncbi.nlm.nih.gov/22600734"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gks412","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gks412","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/nar/gks412","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5085946915","display_name":"Yuki Kato","orcid":"https://orcid.org/0000-0002-1526-2754"},"institutions":[{"id":"https://openalex.org/I75917431","display_name":"Nara Institute of Science and Technology","ror":"https://ror.org/05bhada84","country_code":"JP","type":"education","lineage":["https://openalex.org/I75917431"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Y. Kato","raw_affiliation_strings":["Graduate School of Information Science, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama, Ikoma, Nara 630-0192, Japan. ykato@is.naist.jp","Graduate School of Information Science, Nara Institute of Science and Technology (NAIST) 8916-5 Takayama, Ikoma, Nara 630-0192 Japan"],"affiliations":[{"raw_affiliation_string":"Graduate School of Information Science, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama, Ikoma, Nara 630-0192, Japan. ykato@is.naist.jp","institution_ids":["https://openalex.org/I75917431"]},{"raw_affiliation_string":"Graduate School of Information Science, Nara Institute of Science and Technology (NAIST) 8916-5 Takayama, Ikoma, Nara 630-0192 Japan","institution_ids":["https://openalex.org/I75917431"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076175043","display_name":"Kengo Sato","orcid":"https://orcid.org/0000-0001-6744-7390"},"institutions":[{"id":"https://openalex.org/I73613424","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54","country_code":"JP","type":"government","lineage":["https://openalex.org/I73613424"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"K. Sato","raw_affiliation_strings":["National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan"],"affiliations":[{"raw_affiliation_string":"National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan","institution_ids":["https://openalex.org/I73613424"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082068847","display_name":"Kiyoshi Asai","orcid":"https://orcid.org/0000-0003-0909-4982"},"institutions":[{"id":"https://openalex.org/I73613424","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54","country_code":"JP","type":"government","lineage":["https://openalex.org/I73613424"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"K. Asai","raw_affiliation_strings":["National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan"],"affiliations":[{"raw_affiliation_string":"National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan","institution_ids":["https://openalex.org/I73613424"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016330265","display_name":"Tatsuya Akutsu","orcid":"https://orcid.org/0000-0001-9763-797X"},"institutions":[{"id":"https://openalex.org/I73613424","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54","country_code":"JP","type":"government","lineage":["https://openalex.org/I73613424"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"T. Akutsu","raw_affiliation_strings":["National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan"],"affiliations":[{"raw_affiliation_string":"National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan","institution_ids":["https://openalex.org/I73613424"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5085946915"],"corresponding_institution_ids":["https://openalex.org/I75917431"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":1.6135,"has_fulltext":false,"cited_by_count":30,"citation_normalized_percentile":{"value":0.83160894,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"40","issue":"W1","first_page":"W29","last_page":"W34"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":1.0,"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":1.0,"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":0.9997000098228455,"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":0.998199999332428,"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/rna","display_name":"RNA","score":0.7931560277938843},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6485415697097778},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.6263197064399719},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.6020832657814026},{"id":"https://openalex.org/keywords/integer","display_name":"Integer (computer science)","score":0.5853803157806396},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5048671364784241},{"id":"https://openalex.org/keywords/integer-programming","display_name":"Integer programming","score":0.4716835618019104},{"id":"https://openalex.org/keywords/nucleic-acid-structure","display_name":"Nucleic acid structure","score":0.4699680507183075},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.45319071412086487},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.39722758531570435},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3296734690666199},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.2975887656211853},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.191767156124115},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.16861632466316223},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.12019553780555725},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.07200247049331665}],"concepts":[{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.7931560277938843},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6485415697097778},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.6263197064399719},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.6020832657814026},{"id":"https://openalex.org/C97137487","wikidata":"https://www.wikidata.org/wiki/Q729138","display_name":"Integer (computer science)","level":2,"score":0.5853803157806396},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5048671364784241},{"id":"https://openalex.org/C56086750","wikidata":"https://www.wikidata.org/wiki/Q6042592","display_name":"Integer programming","level":2,"score":0.4716835618019104},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.4699680507183075},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.45319071412086487},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.39722758531570435},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3296734690666199},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2975887656211853},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.191767156124115},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.16861632466316223},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.12019553780555725},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.07200247049331665},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"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":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1093/nar/gks412","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gks412","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:22600734","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22600734","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.783.8975","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.783.8975","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/82/a2/gks412.PMC3394313.pdf","raw_type":"text"},{"id":"pmh:oai:europepmc.org:2409788","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3394313","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:open-archive.highwire.org:nar:40/W1/W29","is_oa":false,"landing_page_url":"http://nar.oxfordjournals.org/cgi/content/short/40/W1/W29","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"},{"id":"pmh:oai:t2r2.star.titech.ac.jp:50744896","is_oa":false,"landing_page_url":"http://t2r2.star.titech.ac.jp/cgi-bin/publicationinfo.cgi?q_publication_content_number=CTT100937974","pdf_url":null,"source":{"id":"https://openalex.org/S4377196385","display_name":"Tokyo Tech Research Repository (Tokyo Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I114531698","host_organization_name":"Tokyo Institute of Technology","host_organization_lineage":["https://openalex.org/I114531698"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1093/nar/gks412","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gks412","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W1966857768","https://openalex.org/W1984675364","https://openalex.org/W1989020100","https://openalex.org/W2020790990","https://openalex.org/W2033677231","https://openalex.org/W2089872148","https://openalex.org/W2102017611","https://openalex.org/W2104702173","https://openalex.org/W2114977400","https://openalex.org/W2115275409","https://openalex.org/W2117552736","https://openalex.org/W2124995041","https://openalex.org/W2130682154","https://openalex.org/W2134489577","https://openalex.org/W2141157874","https://openalex.org/W2142038007","https://openalex.org/W2143407915","https://openalex.org/W2146721220","https://openalex.org/W2148599336","https://openalex.org/W2154085311","https://openalex.org/W2154241726","https://openalex.org/W2160515562"],"related_works":["https://openalex.org/W4286462077","https://openalex.org/W2076804805","https://openalex.org/W4220987767","https://openalex.org/W2038598202","https://openalex.org/W2470187006","https://openalex.org/W2538843585","https://openalex.org/W4320486808","https://openalex.org/W2417242754","https://openalex.org/W3138912362","https://openalex.org/W4285029871"],"abstract_inverted_index":{"We":[0],"present":[1],"a":[2],"web-based":[3],"tool":[4],"set":[5],"Rtips":[6,17,71],"for":[7,27,36],"fast":[8],"and":[9,34],"accurate":[10],"prediction":[11,68],"of":[12],"RNA":[13,29],"2D":[14],"complex":[15],"structures.":[16],"comprises":[18],"two":[19],"computational":[20],"tools":[21],"based":[22],"on":[23,56],"integer":[24],"programming,":[25],"IPknot":[26],"predicting":[28,37],"secondary":[30],"structures":[31],"with":[32,40,52,75],"pseudoknots":[33],"RactIP":[35],"RNA-RNA":[38],"interactions":[39],"kissing":[41],"hairpins.":[42],"Both":[43],"servers":[44],"can":[45],"run":[46],"much":[47],"faster":[48],"than":[49],"existing":[50],"services":[51],"the":[53,76],"same":[54],"purpose":[55],"large":[57],"data":[58],"sets":[59],"as":[60,62],"well":[61],"being":[63],"at":[64,82],"least":[65],"comparable":[66],"in":[67],"accuracy.":[69],"The":[70],"web":[72],"server":[73],"along":[74],"stand-alone":[77],"programs":[78],"is":[79],"freely":[80],"accessible":[81],"http://rna.naist.jp/.":[83]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":2}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}