{"id":"https://openalex.org/W2048104403","doi":"https://doi.org/10.1093/nar/10.1.341","title":"Small changes in free energy assignments for unpaid bases do not affect predicted secondary structures in single stranded RNA","display_name":"Small changes in free energy assignments for unpaid bases do not affect predicted secondary structures in single stranded RNA","publication_year":1982,"publication_date":"1982-01-01","ids":{"openalex":"https://openalex.org/W2048104403","doi":"https://doi.org/10.1093/nar/10.1.341","mag":"2048104403","pmid":"https://pubmed.ncbi.nlm.nih.gov/7063404","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/326137"},"language":"en","primary_location":{"id":"doi:10.1093/nar/10.1.341","doi":"https://doi.org/10.1093/nar/10.1.341","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/10.1.341","pdf_url":"https://academic.oup.com/nar/article-pdf/10/1/341/6959231/10-1-341.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/nar/article-pdf/10/1/341/6959231/10-1-341.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5025357844","display_name":"Ruth Nussinov","orcid":"https://orcid.org/0000-0002-8115-6415","observed_orcids":["https://orcid.org/0000-0002-8115-6415"]},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ruth Nussinov","raw_affiliation_strings":["Department of Chemistry and Laboratory of Chemical Biodynamics, University of California at Berkeley Berkeley, CA 94720"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Laboratory of Chemical Biodynamics, University of California at Berkeley Berkeley, CA 94720","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111538822","display_name":"Ignacio Tinoco","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ignacio Tinoco","raw_affiliation_strings":["Department of Chemistry and Laboratory of Chemical Biodynamics, University of California at Berkeley Berkeley, CA 94720"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Laboratory of Chemical Biodynamics, University of California at Berkeley Berkeley, CA 94720","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5111684908","display_name":"Ann B. Jacobson","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I59553526","display_name":"Stony Brook University","ror":"https://ror.org/05qghxh33","country_code":"US","type":"education","lineage":["https://openalex.org/I59553526"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ann B. Jacobson","raw_affiliation_strings":["Department of Microbiology, State University of New York Stony Brook, NY 11794, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Microbiology, State University of New York Stony Brook, NY 11794, USA","institution_ids":["https://openalex.org/I59553526"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3992,"currency":"USD","value_usd":3992},"apc_paid":null,"fwci":2.1317,"has_fulltext":true,"cited_by_count":27,"citation_normalized_percentile":{"value":0.87581206,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"10","issue":"1","first_page":"341","last_page":"349"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9990000128746033,"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"}},"topics":[{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","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/T10044","display_name":"Protein Structure and Dynamics","score":0.00019999999494757503,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.00019999999494757503,"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-secondary-structure-prediction","display_name":"RNA secondary structure prediction","score":0.9399999976158142},{"id":"https://openalex.org/keywords/mrna-folding","display_name":"mRNA folding","score":0.5360000133514404},{"id":"https://openalex.org/keywords/stem-loop-structure","display_name":"stem-loop structure","score":0.7369999885559082},{"id":"https://openalex.org/keywords/bulge","display_name":"bulge","score":0.9169999957084656},{"id":"https://openalex.org/keywords/internal-loop","display_name":"internal loop","score":0.984000027179718},{"id":"https://openalex.org/keywords/computational-efficiency","display_name":"computational efficiency","score":0.7200000286102295}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8257339000701904},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.7292658090591431},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.6902714371681213},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.6601336598396301},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.6023060083389282},{"id":"https://openalex.org/C512185932","wikidata":"https://www.wikidata.org/wiki/Q28745","display_name":"Nucleotide","level":3,"score":0.5015981197357178},{"id":"https://openalex.org/C186370098","wikidata":"https://www.wikidata.org/wiki/Q442787","display_name":"Energy (signal processing)","level":2,"score":0.45855942368507385},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.4404904246330261},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.3954369127750397},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.386687695980072},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.34182339906692505},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.31830859184265137},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.1934254765510559},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.15113529562950134},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.08614325523376465},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001482","descriptor_name":"Base Composition","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008722","descriptor_name":"Methods","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":true},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/nar/10.1.341","doi":"https://doi.org/10.1093/nar/10.1.341","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/10.1.341","pdf_url":"https://academic.oup.com/nar/article-pdf/10/1/341/6959231/10-1-341.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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":"pmh:oai:pubmedcentral.nih.gov:326137","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/326137","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,"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":"Nucleic Acids Res","raw_type":"Text"},{"id":"pmid:7063404","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/7063404","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":"Nucleic acids research","raw_type":"Comparative Study"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.859.2578","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.859.2578","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/content/10/1/341.full.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/nar/10.1.341","doi":"https://doi.org/10.1093/nar/10.1.341","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/10.1.341","pdf_url":"https://academic.oup.com/nar/article-pdf/10/1/341/6959231/10-1-341.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1702950523","display_name":null,"funder_award_id":"W-7405","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"}],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2048104403.pdf","grobid_xml":"https://content.openalex.org/works/W2048104403.grobid-xml"},"referenced_works_count":9,"referenced_works":["https://openalex.org/W1511465838","https://openalex.org/W1525024558","https://openalex.org/W1981777358","https://openalex.org/W2017302704","https://openalex.org/W2025763720","https://openalex.org/W2028563796","https://openalex.org/W2082135842","https://openalex.org/W2332949416","https://openalex.org/W6820498582"],"related_works":["https://openalex.org/W1526127001","https://openalex.org/W2000191287","https://openalex.org/W2039819958","https://openalex.org/W2059329364","https://openalex.org/W1978187259","https://openalex.org/W4398241221","https://openalex.org/W2040897855","https://openalex.org/W2396713240","https://openalex.org/W2082135842","https://openalex.org/W1559047570"],"abstract_inverted_index":{"We":[0],"present":[1],"extensive":[2],"calculations":[3,81],"of":[4,8,23,31,71],"the":[5,19,28],"secondary":[6,79],"structure":[7,80],"mRNA":[9],"which":[10],"point":[11],"to":[12,15,40,48,76],"its":[13],"insensitivity":[14],"small":[16],"changes":[17],"in":[18,65,85],"free":[20,29],"energy":[21],"assignments":[22],"single":[24,87],"stranded":[25],"regions.":[26],"Truncating":[27],"energies":[30],"hairpin":[32],"loops,":[33],"bulges,":[34],"internal":[35],"loops":[36],"and":[37],"multibranched":[38],"junctions":[39],"two":[41],"significant":[42],"digits":[43],"yields":[44],"structures":[45],"nearly":[46],"identical":[47],"those":[49],"generated":[50],"using":[51],"three":[52],"digit":[53],"values.":[54],"The":[55,69],"results":[56,73],"show":[57],"that":[58],"one":[59],"can":[60],"safely":[61],"use":[62],"truncated":[63],"values":[64],"RNA":[66],"folding":[67],"calculations.":[68],"implementation":[70],"these":[72],"enabled":[74],"us":[75],"carry":[77],"out":[78],"on":[82],"2600":[83],"nucleotides":[84],"a":[86],"computer":[88],"run.":[89]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}