{"id":"https://openalex.org/W1968654140","doi":"https://doi.org/10.1093/nar/gkr207","title":"The RNAmute web server for the mutational analysis of RNA secondary structures","display_name":"The RNAmute web server for the mutational analysis of RNA secondary structures","publication_year":2011,"publication_date":"2011-04-07","ids":{"openalex":"https://openalex.org/W1968654140","doi":"https://doi.org/10.1093/nar/gkr207","mag":"1968654140","pmid":"https://pubmed.ncbi.nlm.nih.gov/21478166"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkr207","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkr207","pdf_url":"https://academic.oup.com/nar/article-pdf/39/suppl_2/W92/7623917/gkr207.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":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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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://academic.oup.com/nar/article-pdf/39/suppl_2/W92/7623917/gkr207.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5028809987","display_name":"Alexander Churkin","orcid":"https://orcid.org/0000-0003-4275-257X"},"institutions":[{"id":"https://openalex.org/I124227911","display_name":"Ben-Gurion University of the Negev","ror":"https://ror.org/05tkyf982","country_code":"IL","type":"education","lineage":["https://openalex.org/I124227911"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"A. Churkin","raw_affiliation_strings":["Department of Computer Science, Ben-Gurion University, Beer-Sheva 84105, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Ben-Gurion University, Beer-Sheva 84105, Israel","institution_ids":["https://openalex.org/I124227911"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038894179","display_name":"Idan Gabdank","orcid":null},"institutions":[{"id":"https://openalex.org/I124227911","display_name":"Ben-Gurion University of the Negev","ror":"https://ror.org/05tkyf982","country_code":"IL","type":"education","lineage":["https://openalex.org/I124227911"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"I. Gabdank","raw_affiliation_strings":["Department of Computer Science, Ben-Gurion University, Beer-Sheva 84105, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Ben-Gurion University, Beer-Sheva 84105, Israel","institution_ids":["https://openalex.org/I124227911"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033583960","display_name":"Danny Barash","orcid":"https://orcid.org/0000-0003-4389-5302"},"institutions":[{"id":"https://openalex.org/I124227911","display_name":"Ben-Gurion University of the Negev","ror":"https://ror.org/05tkyf982","country_code":"IL","type":"education","lineage":["https://openalex.org/I124227911"]}],"countries":["IL"],"is_corresponding":true,"raw_author_name":"D. Barash","raw_affiliation_strings":["Department of Computer Science, Ben-Gurion University, Beer-Sheva 84105, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Ben-Gurion University, Beer-Sheva 84105, Israel","institution_ids":["https://openalex.org/I124227911"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5033583960"],"corresponding_institution_ids":["https://openalex.org/I124227911"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":0.8519,"has_fulltext":false,"cited_by_count":15,"citation_normalized_percentile":{"value":0.70129713,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"39","issue":"suppl","first_page":"W92","last_page":"W99"},"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/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":0.9916999936103821,"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/biology","display_name":"Biology","score":0.8261227607727051},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.7492036819458008},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.6841160655021667},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6619604229927063},{"id":"https://openalex.org/keywords/point-mutation","display_name":"Point mutation","score":0.605771005153656},{"id":"https://openalex.org/keywords/mutagenesis","display_name":"Mutagenesis","score":0.5953944325447083},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5584151744842529},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.5527132153511047},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.5313915014266968},{"id":"https://openalex.org/keywords/protein-secondary-structure","display_name":"Protein secondary structure","score":0.5294069051742554},{"id":"https://openalex.org/keywords/nucleic-acid-structure","display_name":"Nucleic acid structure","score":0.5272414088249207},{"id":"https://openalex.org/keywords/functional-analysis","display_name":"Functional analysis","score":0.5149944424629211},{"id":"https://openalex.org/keywords/sequence-analysis","display_name":"Sequence analysis","score":0.4980032444000244},{"id":"https://openalex.org/keywords/mechanism","display_name":"Mechanism (biology)","score":0.44548407196998596},{"id":"https://openalex.org/keywords/pseudoknot","display_name":"Pseudoknot","score":0.43321558833122253},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.41277194023132324},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.20976987481117249},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.20445775985717773},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1868388056755066},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.09216150641441345},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.07150700688362122}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8261227607727051},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.7492036819458008},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.6841160655021667},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6619604229927063},{"id":"https://openalex.org/C176944494","wikidata":"https://www.wikidata.org/wiki/Q1415380","display_name":"Point mutation","level":4,"score":0.605771005153656},{"id":"https://openalex.org/C16318435","wikidata":"https://www.wikidata.org/wiki/Q149299","display_name":"Mutagenesis","level":4,"score":0.5953944325447083},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5584151744842529},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.5527132153511047},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.5313915014266968},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.5294069051742554},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.5272414088249207},{"id":"https://openalex.org/C55112680","wikidata":"https://www.wikidata.org/wiki/Q190549","display_name":"Functional analysis","level":3,"score":0.5149944424629211},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.4980032444000244},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.44548407196998596},{"id":"https://openalex.org/C105130999","wikidata":"https://www.wikidata.org/wiki/Q414976","display_name":"Pseudoknot","level":4,"score":0.43321558833122253},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.41277194023132324},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.20976987481117249},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.20445775985717773},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1868388056755066},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.09216150641441345},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.07150700688362122},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","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":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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gkr207","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkr207","pdf_url":"https://academic.oup.com/nar/article-pdf/39/suppl_2/W92/7623917/gkr207.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":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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:21478166","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21478166","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:pubmedcentral.nih.gov:3125725","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3125725","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkr207","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkr207","pdf_url":"https://academic.oup.com/nar/article-pdf/39/suppl_2/W92/7623917/gkr207.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":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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320308458","display_name":"American Surgical Association Foundation","ror":"https://ror.org/05grbyt82"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":26,"referenced_works":["https://openalex.org/W1527024319","https://openalex.org/W1543796220","https://openalex.org/W1972708527","https://openalex.org/W1975875487","https://openalex.org/W1978036746","https://openalex.org/W1981167714","https://openalex.org/W1988884185","https://openalex.org/W1992120193","https://openalex.org/W2009818318","https://openalex.org/W2011368877","https://openalex.org/W2017313617","https://openalex.org/W2018414460","https://openalex.org/W2038815243","https://openalex.org/W2054613021","https://openalex.org/W2100039848","https://openalex.org/W2103250001","https://openalex.org/W2105080684","https://openalex.org/W2111652614","https://openalex.org/W2117431427","https://openalex.org/W2131196524","https://openalex.org/W2132034333","https://openalex.org/W2132059579","https://openalex.org/W2138929505","https://openalex.org/W2141157874","https://openalex.org/W2142056356","https://openalex.org/W2149294770"],"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":{"RNA":[0,126,135],"mutational":[1,96,136,183],"analysis":[2,97,184],"at":[3,30,42,187],"the":[4,31,43,47,76,81,112,116,159,163,168],"secondary-structure":[5,127],"level":[6],"can":[7,17],"be":[8,18],"useful":[9],"to":[10,20,38,60,99,145],"a":[11,27,68,88,103],"wide-range":[12],"of":[13,106],"biological":[14],"applications.":[15],"It":[16,138],"used":[19],"predict":[21],"an":[22],"optimal":[23,169],"site":[24],"for":[25,132,175,182],"performing":[26],"nucleotide":[28],"mutation":[29],"single":[32],"molecular":[33],"level,":[34],"as":[35,37,49,87,173],"well":[36],"analyze":[39],"basic":[40],"phenomena":[41],"systems":[44],"level.":[45],"For":[46,80],"former,":[48],"more":[50],"sequence":[51],"modification":[52],"experiments":[53],"are":[54,84,171],"performed":[55],"that":[56,71,119,161],"include":[57],"site-directed":[58],"mutagenesis":[59],"find":[61],"and":[62,95,109,123,166],"explore":[63],"functional":[64],"motifs":[65],"in":[66,74,134],"RNAs,":[67],"pre-processing":[69],"step":[70],"helps":[72],"guide":[73],"planning":[75],"experiment":[77],"becomes":[78],"vital.":[79],"latter,":[82],"mutations":[83,144,148,160],"generally":[85],"accepted":[86],"central":[89],"mechanism":[90],"by":[91,150],"which":[92,157],"evolution":[93],"occurs,":[94],"relating":[98],"structure":[100,121],"should":[101],"gain":[102],"better":[104],"understanding":[105],"system":[107],"functionality":[108],"evolution.":[110],"In":[111],"past":[113],"several":[114],"years,":[115],"program":[117],"RNAmute":[118,179],"is":[120,185],"based":[122],"relies":[124],"on":[125],"prediction":[128],"has":[129,139],"been":[130,140],"developed":[131],"assisting":[133],"analysis.":[137],"extended":[141],"from":[142],"single-point":[143],"treat":[146],"multiple-point":[147],"efficiently":[149],"initially":[151],"calculating":[152],"all":[153],"suboptimal":[154,164],"solutions,":[155],"after":[156],"only":[158],"stabilize":[162],"solutions":[165],"destabilize":[167],"one":[170],"considered":[172],"candidates":[174],"being":[176],"deleterious.":[177],"The":[178],"web":[180],"server":[181],"available":[186],"http://www.cs.bgu.ac.il/~xrnamute/XRNAmute.":[188]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":2}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}
