{"id":"https://openalex.org/W2407134517","doi":"https://doi.org/10.1093/nar/gkw440","title":"<tt>incaRNAfbinv</tt>: a web server for the fragment-based design of RNA sequences","display_name":"<tt>incaRNAfbinv</tt>: a web server for the fragment-based design of RNA sequences","publication_year":2016,"publication_date":"2016-05-16","ids":{"openalex":"https://openalex.org/W2407134517","doi":"https://doi.org/10.1093/nar/gkw440","mag":"2407134517","pmid":"https://pubmed.ncbi.nlm.nih.gov/27185893"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkw440","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkw440","pdf_url":"https://academic.oup.com/nar/article-pdf/44/W1/W308/22933439/gkw440.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/44/W1/W308/22933439/gkw440.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5090841262","display_name":"Matan Drory Retwitzer","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":"Matan Drory\u00a0Retwitzer","raw_affiliation_strings":["Department of Computer Science, Ben-Gurion University, Beer-Sheva 84105, Israel","Department of Computer Science [Beer-Sheva]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Ben-Gurion University, Beer-Sheva 84105, Israel","institution_ids":["https://openalex.org/I124227911"]},{"raw_affiliation_string":"Department of Computer Science [Beer-Sheva]","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089144463","display_name":"Vladimir Reinharz","orcid":"https://orcid.org/0000-0001-8481-1094"},"institutions":[{"id":"https://openalex.org/I4210148697","display_name":"Institute of Bioinformatics","ror":"https://ror.org/04hqfvm50","country_code":"IN","type":"nonprofit","lineage":["https://openalex.org/I4210148697"]},{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA","IN"],"is_corresponding":false,"raw_author_name":"Vladimir Reinharz","raw_affiliation_strings":["School of Computer Science & McGill Centre for Bioinformatics, McGill University, Montr\u00e9al, QC H3A 0E9, Canada","McGill Centre for Bioinformatics","McGill University = Universit\u00e9 McGill [Montr\u00e9al, Canada]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science & McGill Centre for Bioinformatics, McGill University, Montr\u00e9al, QC H3A 0E9, Canada","institution_ids":["https://openalex.org/I5023651"]},{"raw_affiliation_string":"McGill Centre for Bioinformatics","institution_ids":["https://openalex.org/I4210148697"]},{"raw_affiliation_string":"McGill University = Universit\u00e9 McGill [Montr\u00e9al, Canada]","institution_ids":["https://openalex.org/I5023651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076325273","display_name":"Yann Ponty","orcid":"https://orcid.org/0000-0002-7615-3930"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210139461","display_name":"Laboratoire d'Informatique de l'\u00c9cole Polytechnique","ror":"https://ror.org/04afed728","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I142476485","https://openalex.org/I4210139461","https://openalex.org/I4210145102","https://openalex.org/I4210159245"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Yann Ponty","raw_affiliation_strings":["Laboratoire d'Informatique (LIX)-CNRS UMR 7161, \u00c9cole Polytechnique, 91128 Palaiseau, France AMIB team/project, INRIA Saclay, B\u00e2timent Alan Turing, 91128 Palaiseau, France","Algorithms and Models for Integrative Biology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratoire d'Informatique (LIX)-CNRS UMR 7161, \u00c9cole Polytechnique, 91128 Palaiseau, France AMIB team/project, INRIA Saclay, B\u00e2timent Alan Turing, 91128 Palaiseau, France","institution_ids":["https://openalex.org/I4210139461","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"Algorithms and Models for Integrative Biology","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000881484","display_name":"J\u00e9r\u00f4me Waldisp\u00fchl","orcid":"https://orcid.org/0000-0002-2561-7117"},"institutions":[{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"J\u00e9r\u00f4me Waldisp\u00fchl","raw_affiliation_strings":["School of Computer Science & McGill Centre for Bioinformatics, McGill University, Montr\u00e9al, QC H3A 0E9, Canada","McGill University = Universit\u00e9 McGill [Montr\u00e9al, Canada]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science & McGill Centre for Bioinformatics, McGill University, Montr\u00e9al, QC H3A 0E9, Canada","institution_ids":["https://openalex.org/I5023651"]},{"raw_affiliation_string":"McGill University = Universit\u00e9 McGill [Montr\u00e9al, Canada]","institution_ids":["https://openalex.org/I5023651"]}]},{"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":false,"raw_author_name":"Danny Barash","raw_affiliation_strings":["Department of Computer Science, Ben-Gurion University, Beer-Sheva 84105, Israel dbarash@cs.bgu.ac.il","Department of Computer Science [Beer-Sheva]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Ben-Gurion University, Beer-Sheva 84105, Israel dbarash@cs.bgu.ac.il","institution_ids":["https://openalex.org/I124227911"]},{"raw_affiliation_string":"Department of Computer Science [Beer-Sheva]","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":0.5223,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.71355705,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"44","issue":"W1","first_page":"W308","last_page":"W314"},"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":0.9988999962806702,"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":0.996999979019165,"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":0.6805843114852905},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6610699892044067},{"id":"https://openalex.org/keywords/fragment","display_name":"Fragment (logic)","score":0.6275701522827148},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6154837608337402},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.5863606929779053},{"id":"https://openalex.org/keywords/synthetic-biology","display_name":"Synthetic biology","score":0.5320119857788086},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5027873516082764},{"id":"https://openalex.org/keywords/folding","display_name":"Folding (DSP implementation)","score":0.4377380609512329},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.43559974431991577},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3757966160774231},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2271653115749359},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.17236372828483582},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.11830288171768188},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.10547000169754028},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09466522932052612}],"concepts":[{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.6805843114852905},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6610699892044067},{"id":"https://openalex.org/C2776235265","wikidata":"https://www.wikidata.org/wiki/Q18392052","display_name":"Fragment (logic)","level":2,"score":0.6275701522827148},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6154837608337402},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.5863606929779053},{"id":"https://openalex.org/C191908910","wikidata":"https://www.wikidata.org/wiki/Q862838","display_name":"Synthetic biology","level":2,"score":0.5320119857788086},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5027873516082764},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.4377380609512329},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.43559974431991577},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3757966160774231},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2271653115749359},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.17236372828483582},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.11830288171768188},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.10547000169754028},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09466522932052612},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001482","descriptor_name":"Base Composition","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001482","descriptor_name":"Base Composition","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","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":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","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":"D009690","descriptor_name":"Nucleic Acid Conformation","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":"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":"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":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","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},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","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},{"descriptor_ui":"D059370","descriptor_name":"RNA Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059370","descriptor_name":"RNA Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059370","descriptor_name":"RNA Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/nar/gkw440","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkw440","pdf_url":"https://academic.oup.com/nar/article-pdf/44/W1/W308/22933439/gkw440.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:27185893","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27185893","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:HAL:hal-01319682v1","is_oa":true,"landing_page_url":"https://inria.hal.science/hal-01319682","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Research, 2016, 44 (W1), pp.W308 - W314. &#x27E8;10.1093/nar/gkw440&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:europepmc.org:4667656","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5741205","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:44/W1/W308","is_oa":false,"landing_page_url":"http://nar.oxfordjournals.org/cgi/content/short/44/W1/W308","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"}],"best_oa_location":{"id":"doi:10.1093/nar/gkw440","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkw440","pdf_url":"https://academic.oup.com/nar/article-pdf/44/W1/W308/22933439/gkw440.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":[{"score":0.7099999785423279,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320322252","display_name":"Israel Science Foundation","ror":"https://ror.org/04sazxf24"},{"id":"https://openalex.org/F4320323051","display_name":"Ben-Gurion University of the Negev","ror":"https://ror.org/05tkyf982"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2407134517.pdf","grobid_xml":"https://content.openalex.org/works/W2407134517.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W1543796220","https://openalex.org/W1585295485","https://openalex.org/W1669241002","https://openalex.org/W1790782659","https://openalex.org/W1860906034","https://openalex.org/W1969390039","https://openalex.org/W1972139720","https://openalex.org/W1975055709","https://openalex.org/W1978036746","https://openalex.org/W2000775854","https://openalex.org/W2004945910","https://openalex.org/W2006402229","https://openalex.org/W2015960673","https://openalex.org/W2032187763","https://openalex.org/W2039590841","https://openalex.org/W2061770640","https://openalex.org/W2067258168","https://openalex.org/W2073936141","https://openalex.org/W2081630359","https://openalex.org/W2085086400","https://openalex.org/W2089019240","https://openalex.org/W2102020517","https://openalex.org/W2103250001","https://openalex.org/W2104334314","https://openalex.org/W2108230379","https://openalex.org/W2111976294","https://openalex.org/W2115434752","https://openalex.org/W2122944508","https://openalex.org/W2125615424","https://openalex.org/W2130388134","https://openalex.org/W2140505514","https://openalex.org/W2141157874","https://openalex.org/W2143407915","https://openalex.org/W2152678443","https://openalex.org/W2409337327","https://openalex.org/W2426114511","https://openalex.org/W3099817196"],"related_works":["https://openalex.org/W1973480752","https://openalex.org/W2805502594","https://openalex.org/W4253208712","https://openalex.org/W3132641048","https://openalex.org/W2217679042","https://openalex.org/W1603677234","https://openalex.org/W2525971763","https://openalex.org/W2984753899","https://openalex.org/W2783178962","https://openalex.org/W1896179566"],"abstract_inverted_index":{"In":[0,61,148],"recent":[1],"years,":[2],"new":[3],"methods":[4],"for":[5,114,165],"computational":[6],"RNA":[7,36,59,119,131],"design":[8,57,67,123,152],"have":[9],"been":[10],"developed":[11],"and":[12,20,47,109,136,145,178,183],"applied":[13],"to":[14,150],"various":[15],"problems":[16],"in":[17,27,107,186],"synthetic":[18,154],"biology":[19],"nanotechnology.":[21],"Lately,":[22],"there":[23],"is":[24,48,88],"considerable":[25],"interest":[26],"incorporating":[28],"essential":[29],"biological":[30],"information":[31],"when":[32],"solving":[33],"the":[34,49,66,77,82,92,104,115,151,166],"inverse":[35,116],"folding":[37,117],"problem.":[38],"Correspondingly,":[39],"RNAfbinv":[40,108,177],"aims":[41],"at":[42,192],"including":[43],"biologically":[44],"meaningful":[45],"constraints":[46],"only":[50],"program":[51],"to-date":[52],"that":[53,70],"performs":[54],"a":[55,121,129,162],"fragment-based":[56,122],"of":[58,68,96,118,153,168],"sequences.":[60],"doing":[62],"so":[63],"it":[64,157],"allows":[65],"sequences":[69],"do":[71],"not":[72],"necessarily":[73],"exactly":[74],"fold":[75],"into":[76],"target,":[78],"as":[79,81,127,161],"long":[80],"overall":[83],"coarse-grained":[84],"tree":[85],"graph":[86],"shape":[87],"preserved.":[89],"Augmented":[90],"by":[91],"weighted":[93],"sampling":[94],"algorithm":[95],"incaRNAtion,":[97],"our":[98,187],"web":[99,188],"server":[100,189],"called":[101],"incaRNAfbinv":[102],"implements":[103],"method":[105],"devised":[106],"offers":[110],"an":[111],"interactive":[112],"environment":[113],"using":[120],"approach.":[124],"It":[125],"takes":[126],"input:":[128],"target":[130,140],"secondary":[132],"structure;":[133],"optional":[134,139],"sequence":[135],"motif":[137],"constraints;":[138],"minimum":[141],"free":[142],"energy,":[143],"neutrality":[144],"GC":[146],"content.":[147],"addition":[149],"regulatory":[155],"sequences,":[156],"can":[158],"be":[159],"used":[160],"pre-processing":[163],"step":[164],"detection":[167],"novel":[169],"natural":[170],"occurring":[171],"RNAs.":[172],"The":[173],"two":[174],"complementary":[175],"methodologies":[176],"incaRNAtion":[179],"are":[180],"merged":[181],"together":[182],"fully":[184],"implemented":[185],"incaRNAfbinv,":[190],"available":[191],"http://www.cs.bgu.ac.il/incaRNAfbinv.":[193]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":2}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2016-06-24T00:00:00"}
