{"id":"https://openalex.org/W1512182242","doi":"https://doi.org/10.1186/1471-2105-16-s9-s6","title":"Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations","display_name":"Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations","publication_year":2015,"publication_date":"2015-06-01","ids":{"openalex":"https://openalex.org/W1512182242","doi":"https://doi.org/10.1186/1471-2105-16-s9-s6","mag":"1512182242","pmid":"https://pubmed.ncbi.nlm.nih.gov/26051557"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-16-s9-s6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-16-s9-s6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-16-S9-S6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-16-S9-S6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Francesco Di Palma","orcid":null},"institutions":[{"id":"https://openalex.org/I138549579","display_name":"Scuola Internazionale Superiore di Studi Avanzati","ror":"https://ror.org/004fze387","country_code":"IT","type":"education","lineage":["https://openalex.org/I138549579"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Francesco Di Palma","raw_affiliation_strings":["SISSA, Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea, 265, 32136, Trieste, Italy"],"affiliations":[{"raw_affiliation_string":"SISSA, Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea, 265, 32136, Trieste, Italy","institution_ids":["https://openalex.org/I138549579"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Sandro Bottaro","orcid":null},"institutions":[{"id":"https://openalex.org/I138549579","display_name":"Scuola Internazionale Superiore di Studi Avanzati","ror":"https://ror.org/004fze387","country_code":"IT","type":"education","lineage":["https://openalex.org/I138549579"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Sandro Bottaro","raw_affiliation_strings":["SISSA, Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea, 265, 32136, Trieste, Italy"],"affiliations":[{"raw_affiliation_string":"SISSA, Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea, 265, 32136, Trieste, Italy","institution_ids":["https://openalex.org/I138549579"]}]},{"author_position":"last","author":{"id":null,"display_name":"Giovanni Bussi","orcid":null},"institutions":[{"id":"https://openalex.org/I138549579","display_name":"Scuola Internazionale Superiore di Studi Avanzati","ror":"https://ror.org/004fze387","country_code":"IT","type":"education","lineage":["https://openalex.org/I138549579"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Giovanni Bussi","raw_affiliation_strings":["SISSA, Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea, 265, 32136, Trieste, Italy"],"affiliations":[{"raw_affiliation_string":"SISSA, Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea, 265, 32136, Trieste, Italy","institution_ids":["https://openalex.org/I138549579"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I138549579"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":2.1127,"has_fulltext":true,"cited_by_count":31,"citation_normalized_percentile":{"value":0.86828768,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"16","issue":"S9","first_page":"S6","last_page":"S6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9097999930381775,"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":0.9097999930381775,"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":0.0066999997943639755,"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":0.006000000052154064,"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/initialization","display_name":"Initialization","score":0.6913999915122986},{"id":"https://openalex.org/keywords/sampling","display_name":"Sampling (signal processing)","score":0.6335999965667725},{"id":"https://openalex.org/keywords/protocol","display_name":"Protocol (science)","score":0.5041999816894531},{"id":"https://openalex.org/keywords/umbrella-sampling","display_name":"Umbrella sampling","score":0.4925000071525574},{"id":"https://openalex.org/keywords/loop","display_name":"Loop (graph theory)","score":0.47290000319480896},{"id":"https://openalex.org/keywords/stability","display_name":"Stability (learning theory)","score":0.41839998960494995},{"id":"https://openalex.org/keywords/interpretation","display_name":"Interpretation (philosophy)","score":0.39010000228881836}],"concepts":[{"id":"https://openalex.org/C114466953","wikidata":"https://www.wikidata.org/wiki/Q6034165","display_name":"Initialization","level":2,"score":0.6913999915122986},{"id":"https://openalex.org/C140779682","wikidata":"https://www.wikidata.org/wiki/Q210868","display_name":"Sampling (signal processing)","level":3,"score":0.6335999965667725},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6154000163078308},{"id":"https://openalex.org/C2780385302","wikidata":"https://www.wikidata.org/wiki/Q367158","display_name":"Protocol (science)","level":3,"score":0.5041999816894531},{"id":"https://openalex.org/C128747166","wikidata":"https://www.wikidata.org/wiki/Q7881414","display_name":"Umbrella sampling","level":3,"score":0.4925000071525574},{"id":"https://openalex.org/C184670325","wikidata":"https://www.wikidata.org/wiki/Q512604","display_name":"Loop (graph theory)","level":2,"score":0.47290000319480896},{"id":"https://openalex.org/C112972136","wikidata":"https://www.wikidata.org/wiki/Q7595718","display_name":"Stability (learning theory)","level":2,"score":0.41839998960494995},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4138999879360199},{"id":"https://openalex.org/C527412718","wikidata":"https://www.wikidata.org/wiki/Q855395","display_name":"Interpretation (philosophy)","level":2,"score":0.39010000228881836},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.3871000111103058},{"id":"https://openalex.org/C2776291640","wikidata":"https://www.wikidata.org/wiki/Q2912517","display_name":"Value (mathematics)","level":2,"score":0.3573000133037567},{"id":"https://openalex.org/C52740198","wikidata":"https://www.wikidata.org/wiki/Q1539564","display_name":"Importance sampling","level":3,"score":0.3495999872684479},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.31049999594688416},{"id":"https://openalex.org/C61797465","wikidata":"https://www.wikidata.org/wiki/Q1188986","display_name":"Term (time)","level":2,"score":0.3100999891757965},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.2985999882221222},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.2955000102519989},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2888000011444092},{"id":"https://openalex.org/C148043351","wikidata":"https://www.wikidata.org/wiki/Q4456944","display_name":"Current (fluid)","level":2,"score":0.28380000591278076},{"id":"https://openalex.org/C2777317252","wikidata":"https://www.wikidata.org/wiki/Q18393516","display_name":"Rare events","level":2,"score":0.27320000529289246},{"id":"https://openalex.org/C70636015","wikidata":"https://www.wikidata.org/wiki/Q4300350","display_name":"Molecular biophysics","level":2,"score":0.2662999927997589},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.25369998812675476},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.2529999911785126}],"mesh":[{"descriptor_ui":"D000225","descriptor_name":"Adenine","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000225","descriptor_name":"Adenine","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000225","descriptor_name":"Adenine","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"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":"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":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058928","descriptor_name":"Riboswitch","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D058928","descriptor_name":"Riboswitch","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D058928","descriptor_name":"Riboswitch","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-16-s9-s6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-16-s9-s6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-16-S9-S6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26051557","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26051557","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:arXiv.org:1504.07392","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1504.07392","pdf_url":"https://arxiv.org/pdf/1504.07392","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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:europepmc.org:3443205","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4464220","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-16-s9-s6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-16-s9-s6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-16-S9-S6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2761285720","display_name":null,"funder_award_id":"FP/2007-2013","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G3981126665","display_name":null,"funder_award_id":"Seventh Framework Programme","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G5593277320","display_name":null,"funder_award_id":"2007-2013","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8051717526","display_name":null,"funder_award_id":"Grant","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8172532997","display_name":"Small ribonucleic acids in silico","funder_award_id":"306662","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1512182242.pdf","grobid_xml":"https://content.openalex.org/works/W1512182242.grobid-xml"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W1966871849","https://openalex.org/W1967737979","https://openalex.org/W1972708527","https://openalex.org/W1976161355","https://openalex.org/W1976499671","https://openalex.org/W1991667171","https://openalex.org/W1993177346","https://openalex.org/W2003240840","https://openalex.org/W2021931103","https://openalex.org/W2035266068","https://openalex.org/W2037199390","https://openalex.org/W2042090376","https://openalex.org/W2048683276","https://openalex.org/W2051564388","https://openalex.org/W2054713699","https://openalex.org/W2057477511","https://openalex.org/W2059668879","https://openalex.org/W2060419010","https://openalex.org/W2066803038","https://openalex.org/W2067174909","https://openalex.org/W2067258168","https://openalex.org/W2067810191","https://openalex.org/W2071573742","https://openalex.org/W2076943973","https://openalex.org/W2078051106","https://openalex.org/W2081046982","https://openalex.org/W2086817352","https://openalex.org/W2088892367","https://openalex.org/W2089200960","https://openalex.org/W2100596347","https://openalex.org/W2112154906","https://openalex.org/W2117223714","https://openalex.org/W2122774834","https://openalex.org/W2123412671","https://openalex.org/W2128572087","https://openalex.org/W2131288855","https://openalex.org/W2132920850","https://openalex.org/W2136729627","https://openalex.org/W2138825634","https://openalex.org/W2141309294","https://openalex.org/W2141857874","https://openalex.org/W2145958275","https://openalex.org/W2146411229","https://openalex.org/W2147993766","https://openalex.org/W2153178417","https://openalex.org/W2158073100","https://openalex.org/W2160544821"],"related_works":[],"abstract_inverted_index":{"Kissing":[0],"complex":[1],"stabilization":[2],"given":[3],"by":[4],"the":[5,14,20,24,32,36],"ligand":[6],"was":[7],"compatible":[8],"with":[9],"available":[10],"experimental":[11],"data.":[12],"However,":[13],"dependence":[15],"of":[16,23,35],"its":[17],"value":[18],"on":[19,31],"initialization":[21],"protocol":[22],"umbrella":[25],"sampling":[26,44],"simulations":[27],"posed":[28],"some":[29],"questions":[30],"quantitative":[33],"interpretation":[34],"results":[37],"and":[38],"called":[39],"for":[40],"better":[41],"converged":[42],"enhanced":[43],"simulations.":[45]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":6}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2016-06-24T00:00:00"}
