{"id":"https://openalex.org/W2076756368","doi":"https://doi.org/10.1089/106652700750050862","title":"RNA Pseudoknot Prediction in Energy-Based Models","display_name":"RNA Pseudoknot Prediction in Energy-Based Models","publication_year":2000,"publication_date":"2000-08-01","ids":{"openalex":"https://openalex.org/W2076756368","doi":"https://doi.org/10.1089/106652700750050862","mag":"2076756368","pmid":"https://pubmed.ncbi.nlm.nih.gov/11108471"},"language":"en","primary_location":{"id":"doi:10.1089/106652700750050862","doi":"https://doi.org/10.1089/106652700750050862","is_oa":false,"landing_page_url":"https://doi.org/10.1089/106652700750050862","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-1"],"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443","https://openalex.org/P4310320017"],"host_organization_lineage_names":["Mary Ann Liebert, Inc.","SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5084872691","display_name":"Rune B. Lyngs\u00f8","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I185103710","display_name":"University of California, Santa Cruz","ror":"https://ror.org/03s65by71","country_code":"US","type":"education","lineage":["https://openalex.org/I185103710"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rune B. Lyngs\u00f8","raw_affiliation_strings":["Baskin Center for Computer Science and Engineering, University of California, Santa Cruz, CA 95064","Baskin Center for Computer Science and Engineering, University of California, Santa Cruz 95064, USA. rlyngsoe@cse.ucsc.edu"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Baskin Center for Computer Science and Engineering, University of California, Santa Cruz, CA 95064","institution_ids":["https://openalex.org/I185103710"]},{"raw_affiliation_string":"Baskin Center for Computer Science and Engineering, University of California, Santa Cruz 95064, USA. rlyngsoe@cse.ucsc.edu","institution_ids":["https://openalex.org/I185103710"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5113716245","display_name":"Christian N. S. Pedersen","orcid":"https://orcid.org/0000-0002-8947-6771","observed_orcids":["https://orcid.org/0000-0002-8947-6771"]},"institutions":[{"id":"https://openalex.org/I204337017","display_name":"Aarhus University","ror":"https://ror.org/01aj84f44","country_code":"DK","type":"education","lineage":["https://openalex.org/I204337017"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Christian N. S. Pedersen","raw_affiliation_strings":["Basic Research In Computer Science (BRICS), Department of Computer Science, University of Aarhus, DK8000 \u00c5rhus, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Basic Research In Computer Science (BRICS), Department of Computer Science, University of Aarhus, DK8000 \u00c5rhus, Denmark","institution_ids":["https://openalex.org/I204337017"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.0949,"has_fulltext":false,"cited_by_count":359,"citation_normalized_percentile":{"value":0.74537731,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"7","issue":"3-4","first_page":"409","last_page":"427"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9965999722480774,"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":0.9965999722480774,"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/T11269","display_name":"Algorithms and Data Compression","score":0.0007999999797903001,"subfield":{"id":"https://openalex.org/subfields/2614","display_name":"Theoretical Computer Science"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12029","display_name":"DNA and Biological Computing","score":0.0003000000142492354,"subfield":{"id":"https://openalex.org/subfields/2614","display_name":"Theoretical Computer Science"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/rna-pseudoknots","display_name":"RNA pseudoknots","score":0.8830000162124634},{"id":"https://openalex.org/keywords/rna-secondary-structure-prediction","display_name":"RNA secondary structure prediction","score":0.9959999918937683},{"id":"https://openalex.org/keywords/energy-based-models","display_name":"energy-based models","score":0.9229999780654907},{"id":"https://openalex.org/keywords/free-energy-minimization","display_name":"free energy minimization","score":0.9869999885559082},{"id":"https://openalex.org/keywords/np-completeness","display_name":"NP-completeness","score":0.8349999785423279},{"id":"https://openalex.org/keywords/computational-complexity","display_name":"computational complexity","score":0.8299999833106995}],"concepts":[{"id":"https://openalex.org/C105130999","wikidata":"https://www.wikidata.org/wiki/Q414976","display_name":"Pseudoknot","level":4,"score":0.9368568658828735},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.7392857074737549},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.683887243270874},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.5239272713661194},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5097977519035339},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.48800864815711975},{"id":"https://openalex.org/C14961307","wikidata":"https://www.wikidata.org/wiki/Q5377176","display_name":"Energy minimization","level":2,"score":0.45859187841415405},{"id":"https://openalex.org/C311688","wikidata":"https://www.wikidata.org/wiki/Q2393193","display_name":"Time complexity","level":2,"score":0.4392364025115967},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.40055975317955017},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.33316224813461304},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3244274854660034},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3059200644493103},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2310500144958496},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.18240687251091003},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10387158393859863},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.08808502554893494},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1089/106652700750050862","doi":"https://doi.org/10.1089/106652700750050862","is_oa":false,"landing_page_url":"https://doi.org/10.1089/106652700750050862","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-1"],"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443","https://openalex.org/P4310320017"],"host_organization_lineage_names":["Mary Ann Liebert, Inc.","SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},{"id":"pmid:11108471","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/11108471","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,"listed_in":[],"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 computational biology : a journal of computational molecular cell biology","raw_type":"Journal Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.34.4044","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.34.4044","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.cse.ucsc.edu/~rlyngsoe/jcb.ps","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W1968245790","https://openalex.org/W1976373002","https://openalex.org/W1981777358","https://openalex.org/W1984675364","https://openalex.org/W1993968482","https://openalex.org/W2000191287","https://openalex.org/W2009818318","https://openalex.org/W2011368877","https://openalex.org/W2013465290","https://openalex.org/W2017302704","https://openalex.org/W2023206235","https://openalex.org/W2025763720","https://openalex.org/W2028574527","https://openalex.org/W2045895660","https://openalex.org/W2050110866","https://openalex.org/W2054931730","https://openalex.org/W2075702353","https://openalex.org/W2086509077","https://openalex.org/W2095145214","https://openalex.org/W2109297587","https://openalex.org/W2123241418","https://openalex.org/W2124162379","https://openalex.org/W2146922921","https://openalex.org/W2161381662","https://openalex.org/W2165654401","https://openalex.org/W2398951942","https://openalex.org/W2795615963","https://openalex.org/W2997317337"],"related_works":["https://openalex.org/W2028574527","https://openalex.org/W2796011749","https://openalex.org/W2247236880","https://openalex.org/W4300678633","https://openalex.org/W7099271846","https://openalex.org/W2786729541","https://openalex.org/W7100267668","https://openalex.org/W2036643266","https://openalex.org/W2062772609","https://openalex.org/W2807635396"],"abstract_inverted_index":{"RNA":[0,24,71,92,106],"molecules":[1],"are":[2],"sequences":[3],"of":[4,23,69,87,104,118,121],"nucleotides":[5],"that":[6,34,50,100],"serve":[7],"as":[8,18],"more":[9],"than":[10],"mere":[11],"intermediaries":[12],"between":[13],"DNA":[14],"and":[15,59],"proteins,":[16],"e.g.,":[17],"catalytic":[19],"molecules.":[20],"Computational":[21],"prediction":[22,32],"secondary":[25,72,93,107],"structure":[26,31],"is":[27,111],"among":[28],"the":[29,67,101],"few":[30],"problems":[33],"can":[35],"be":[36],"solved":[37],"satisfactorily":[38],"in":[39],"polynomial":[40],"time.":[41],"Most":[42],"work":[43],"has":[44],"been":[45],"done":[46],"to":[47],"predict":[48],"structures":[49,73,94,108],"do":[51],"not":[52],"contain":[53],"pseudoknots.":[54,96,122],"Allowing":[55],"pseudoknots":[56,75,110],"introduces":[57],"modeling":[58],"computational":[60],"problems.":[61],"In":[62],"this":[63],"paper":[64],"we":[65],"consider":[66],"problem":[68,103],"predicting":[70,91,105],"with":[74,95],"based":[76],"on":[77],"free":[78],"energy":[79],"minimization.":[80],"We":[81,97],"first":[82],"give":[83],"a":[84,115],"brief":[85],"comparison":[86],"energy-based":[88],"methods":[89],"for":[90,114],"then":[98],"prove":[99],"general":[102],"containing":[109],"NP":[112],"complete":[113],"large":[116],"class":[117],"reasonable":[119],"models":[120]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":26},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":26},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":10},{"year":2017,"cited_by_count":12},{"year":2016,"cited_by_count":11},{"year":2015,"cited_by_count":16},{"year":2014,"cited_by_count":11},{"year":2013,"cited_by_count":15},{"year":2012,"cited_by_count":21}],"updated_date":"2026-11-07T11:25:07.637180","created_date":"2016-06-24T00:00:00"}