{"id":"https://openalex.org/W2595313367","doi":"https://doi.org/10.1093/bioinformatics/btx127","title":"Fast, clash-free RNA conformational morphing using molecular junctions","display_name":"Fast, clash-free RNA conformational morphing using molecular junctions","publication_year":2017,"publication_date":"2017-03-12","ids":{"openalex":"https://openalex.org/W2595313367","doi":"https://doi.org/10.1093/bioinformatics/btx127","mag":"2595313367","pmid":"https://pubmed.ncbi.nlm.nih.gov/28334257"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx127","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx127","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/14/2114/25157056/btx127.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/33/14/2114/25157056/btx127.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5023095596","display_name":"Am\u00e9lie H\u00e9liou","orcid":null},"institutions":[{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I142476485","display_name":"\u00c9cole Polytechnique","ror":"https://ror.org/05hy3tk52","country_code":"FR","type":"education","lineage":["https://openalex.org/I142476485","https://openalex.org/I4210145102"]},{"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":true,"raw_author_name":"Am\u00e9lie H\u00e9liou","raw_affiliation_strings":["LIX, Ecole Polytechnique, CNRS, Inria, Universit\u00e9 Paris-Saclay, Palaiseau, France","Algorithms and Models for Integrative Biology"],"affiliations":[{"raw_affiliation_string":"LIX, Ecole Polytechnique, CNRS, Inria, Universit\u00e9 Paris-Saclay, Palaiseau, France","institution_ids":["https://openalex.org/I277688954","https://openalex.org/I4210139461","https://openalex.org/I142476485","https://openalex.org/I1294671590"]},{"raw_affiliation_string":"Algorithms and Models for Integrative Biology","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007316487","display_name":"Dominik Budday","orcid":"https://orcid.org/0000-0002-6180-2125"},"institutions":[{"id":"https://openalex.org/I181369854","display_name":"Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg","ror":"https://ror.org/00f7hpc57","country_code":"DE","type":"education","lineage":["https://openalex.org/I181369854"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Dominik Budday","raw_affiliation_strings":["Chair of Applied Dynamics, University of Erlangen-Nuremberg, Erlangen, Germany"],"affiliations":[{"raw_affiliation_string":"Chair of Applied Dynamics, University of Erlangen-Nuremberg, Erlangen, Germany","institution_ids":["https://openalex.org/I181369854"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060357309","display_name":"Rasmus Fonseca","orcid":"https://orcid.org/0000-0002-8322-4880"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]},{"id":"https://openalex.org/I2801935854","display_name":"SLAC National Accelerator Laboratory","ror":"https://ror.org/05gzmn429","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I2801935854","https://openalex.org/I39565521","https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rasmus Fonseca","raw_affiliation_strings":["Biosciences Division, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA","Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA"],"affiliations":[{"raw_affiliation_string":"Biosciences Division, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA","institution_ids":["https://openalex.org/I2801935854","https://openalex.org/I97018004"]},{"raw_affiliation_string":"Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5024202025","display_name":"Henry van den Bedem","orcid":"https://orcid.org/0000-0003-2358-841X"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]},{"id":"https://openalex.org/I2801935854","display_name":"SLAC National Accelerator Laboratory","ror":"https://ror.org/05gzmn429","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I2801935854","https://openalex.org/I39565521","https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Henry van den Bedem","raw_affiliation_strings":["Biosciences Division, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA"],"affiliations":[{"raw_affiliation_string":"Biosciences Division, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA","institution_ids":["https://openalex.org/I2801935854","https://openalex.org/I97018004"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5023095596"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I142476485","https://openalex.org/I277688954","https://openalex.org/I4210139461"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.3357,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.58968893,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"33","issue":"14","first_page":"2114","last_page":"2122"},"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/T10604","display_name":"RNA Research and Splicing","score":0.9998000264167786,"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":0.9998000264167786,"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/morphing","display_name":"Morphing","score":0.9331862926483154},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.6160075068473816},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5231707692146301},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.3489508032798767},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3310135006904602},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.30660977959632874},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.24034634232521057},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20016255974769592},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.14426890015602112},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13709759712219238}],"concepts":[{"id":"https://openalex.org/C50637493","wikidata":"https://www.wikidata.org/wiki/Q1136781","display_name":"Morphing","level":2,"score":0.9331862926483154},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.6160075068473816},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5231707692146301},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.3489508032798767},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3310135006904602},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.30660977959632874},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.24034634232521057},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20016255974769592},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.14426890015602112},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13709759712219238}],"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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":"D008958","descriptor_name":"Models, Molecular","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":"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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btx127","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx127","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/14/2114/25157056/btx127.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:28334257","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28334257","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:HAL:hal-01569620v1","is_oa":false,"landing_page_url":"https://hal.science/hal-01569620","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 2017, 33 (14), pp.2114 - 2122. &#x27E8;10.1093/bioinformatics/btx127&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:osti.gov:1352493","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1352493","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"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":null},{"id":"pmh:oai:osti.gov:1368458","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1368458","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"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":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btx127","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx127","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/14/2114/25157056/btx127.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/16","display_name":"Peace, Justice and strong institutions","score":0.800000011920929}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2595313367.pdf","grobid_xml":"https://content.openalex.org/works/W2595313367.grobid-xml"},"referenced_works_count":50,"referenced_works":["https://openalex.org/W1513228388","https://openalex.org/W1556977774","https://openalex.org/W1672171675","https://openalex.org/W1971218796","https://openalex.org/W1985490516","https://openalex.org/W1987262986","https://openalex.org/W1988409793","https://openalex.org/W1992917343","https://openalex.org/W2014790936","https://openalex.org/W2021937561","https://openalex.org/W2025190578","https://openalex.org/W2033676066","https://openalex.org/W2035626375","https://openalex.org/W2039143660","https://openalex.org/W2051536237","https://openalex.org/W2058094839","https://openalex.org/W2058276221","https://openalex.org/W2059099058","https://openalex.org/W2069165607","https://openalex.org/W2069779808","https://openalex.org/W2070777085","https://openalex.org/W2079983771","https://openalex.org/W2080026723","https://openalex.org/W2081894427","https://openalex.org/W2086115719","https://openalex.org/W2091705944","https://openalex.org/W2103589755","https://openalex.org/W2103939914","https://openalex.org/W2105371577","https://openalex.org/W2106632741","https://openalex.org/W2114850508","https://openalex.org/W2122326469","https://openalex.org/W2123733285","https://openalex.org/W2130479394","https://openalex.org/W2144857097","https://openalex.org/W2145477667","https://openalex.org/W2154714625","https://openalex.org/W2158114027","https://openalex.org/W2164548935","https://openalex.org/W2171605109","https://openalex.org/W2192499203","https://openalex.org/W2199584576","https://openalex.org/W2203997369","https://openalex.org/W2236230312","https://openalex.org/W2266228788","https://openalex.org/W2289835977","https://openalex.org/W2341963847","https://openalex.org/W2487638977","https://openalex.org/W2949983130","https://openalex.org/W6637288986"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W1679315481","https://openalex.org/W3151495635","https://openalex.org/W2527526854","https://openalex.org/W4236870338","https://openalex.org/W2062208111"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
