{"id":"https://openalex.org/W1971003569","doi":"https://doi.org/10.3390/a2010200","title":"Exhaustive Enumeration of Kinetic Model Topologies for the Analysis of Time-Resolved RNA Folding","display_name":"Exhaustive Enumeration of Kinetic Model Topologies for the Analysis of Time-Resolved RNA Folding","publication_year":2009,"publication_date":"2009-02-10","ids":{"openalex":"https://openalex.org/W1971003569","doi":"https://doi.org/10.3390/a2010200","mag":"1971003569","pmid":"https://pubmed.ncbi.nlm.nih.gov/19865589"},"language":"en","primary_location":{"id":"doi:10.3390/a2010200","is_oa":true,"landing_page_url":"https://doi.org/10.3390/a2010200","pdf_url":"https://www.mdpi.com/1999-4893/2/1/200/pdf?version=1234960336","source":{"id":"https://openalex.org/S190629608","display_name":"Algorithms","issn_l":"1999-4893","issn":["1999-4893"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/1999-4893/2/1/200/pdf?version=1234960336","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022863916","display_name":"Joshua S. Martin","orcid":null},"institutions":[{"id":"https://openalex.org/I1339417872","display_name":"Wadsworth Center","ror":"https://ror.org/050kf9c55","country_code":"US","type":"facility","lineage":["https://openalex.org/I1298060332","https://openalex.org/I1339417872"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Joshua  S. Martin","raw_affiliation_strings":["Computational and Structural Biology Department, Wadsworth Center, Albany, NY 12208, USA"],"affiliations":[{"raw_affiliation_string":"Computational and Structural Biology Department, Wadsworth Center, Albany, NY 12208, USA","institution_ids":["https://openalex.org/I1339417872"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066320405","display_name":"Katrina Simmons","orcid":null},"institutions":[{"id":"https://openalex.org/I1339417872","display_name":"Wadsworth Center","ror":"https://ror.org/050kf9c55","country_code":"US","type":"facility","lineage":["https://openalex.org/I1298060332","https://openalex.org/I1339417872"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Katrina Simmons","raw_affiliation_strings":["Computational and Structural Biology Department, Wadsworth Center, Albany, NY 12208, USA"],"affiliations":[{"raw_affiliation_string":"Computational and Structural Biology Department, Wadsworth Center, Albany, NY 12208, USA","institution_ids":["https://openalex.org/I1339417872"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5026069604","display_name":"Alain Laederach","orcid":"https://orcid.org/0000-0002-5088-9907"},"institutions":[{"id":"https://openalex.org/I1339417872","display_name":"Wadsworth Center","ror":"https://ror.org/050kf9c55","country_code":"US","type":"facility","lineage":["https://openalex.org/I1298060332","https://openalex.org/I1339417872"]},{"id":"https://openalex.org/I392282","display_name":"University at Albany, State University of New York","ror":"https://ror.org/012zs8222","country_code":"US","type":"education","lineage":["https://openalex.org/I392282"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alain Laederach","raw_affiliation_strings":["Biomedical Sciences Program, School of Public Health, SUNY, Albany, NY 12201, USA","Computational and Structural Biology Department, Wadsworth Center, Albany, NY 12208, USA"],"affiliations":[{"raw_affiliation_string":"Biomedical Sciences Program, School of Public Health, SUNY, Albany, NY 12201, USA","institution_ids":["https://openalex.org/I392282"]},{"raw_affiliation_string":"Computational and Structural Biology Department, Wadsworth Center, Albany, NY 12208, USA","institution_ids":["https://openalex.org/I1339417872"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5022863916"],"corresponding_institution_ids":["https://openalex.org/I1339417872"],"apc_list":{"value":1400,"currency":"CHF","value_usd":1515},"apc_paid":{"value":1400,"currency":"CHF","value_usd":1515},"fwci":0.6719,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.67949053,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"2","issue":"1","first_page":"200","last_page":"214"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998000264167786,"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"}},"topics":[{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.996399998664856,"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":0.9930999875068665,"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/degeneracy","display_name":"Degeneracy (biology)","score":0.7898931503295898},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6415688395500183},{"id":"https://openalex.org/keywords/footprinting","display_name":"Footprinting","score":0.5735727548599243},{"id":"https://openalex.org/keywords/kinetic-energy","display_name":"Kinetic energy","score":0.4273582100868225},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.40052908658981323},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.39975354075431824},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3747069239616394},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.27468013763427734},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.251268208026886},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.1847425401210785},{"id":"https://openalex.org/keywords/base-sequence","display_name":"Base sequence","score":0.17565637826919556},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10953724384307861}],"concepts":[{"id":"https://openalex.org/C2777727622","wikidata":"https://www.wikidata.org/wiki/Q5251772","display_name":"Degeneracy (biology)","level":2,"score":0.7898931503295898},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6415688395500183},{"id":"https://openalex.org/C2778021871","wikidata":"https://www.wikidata.org/wiki/Q648006","display_name":"Footprinting","level":4,"score":0.5735727548599243},{"id":"https://openalex.org/C135889238","wikidata":"https://www.wikidata.org/wiki/Q46276","display_name":"Kinetic energy","level":2,"score":0.4273582100868225},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.40052908658981323},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.39975354075431824},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3747069239616394},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.27468013763427734},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.251268208026886},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.1847425401210785},{"id":"https://openalex.org/C3017666073","wikidata":"https://www.wikidata.org/wiki/Q1764062","display_name":"Base sequence","level":3,"score":0.17565637826919556},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10953724384307861},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3390/a2010200","is_oa":true,"landing_page_url":"https://doi.org/10.3390/a2010200","pdf_url":"https://www.mdpi.com/1999-4893/2/1/200/pdf?version=1234960336","source":{"id":"https://openalex.org/S190629608","display_name":"Algorithms","issn_l":"1999-4893","issn":["1999-4893"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms","raw_type":"journal-article"},{"id":"pmid:19865589","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19865589","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":"Algorithms","raw_type":null},{"id":"pmh:oai:doaj.org/article:ad01ba2833e144e3b43ee4078e4e615a","is_oa":true,"landing_page_url":"https://doaj.org/article/ad01ba2833e144e3b43ee4078e4e615a","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms, Vol 2, Iss 1, Pp 200-214 (2009)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2768297","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2768297","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3390/a2010200","is_oa":true,"landing_page_url":"https://doi.org/10.3390/a2010200","pdf_url":"https://www.mdpi.com/1999-4893/2/1/200/pdf?version=1234960336","source":{"id":"https://openalex.org/S190629608","display_name":"Algorithms","issn_l":"1999-4893","issn":["1999-4893"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1971003569.pdf","grobid_xml":"https://content.openalex.org/works/W1971003569.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W1970441908","https://openalex.org/W1976638553","https://openalex.org/W1982511846","https://openalex.org/W1984072183","https://openalex.org/W1986103734","https://openalex.org/W1986581714","https://openalex.org/W2006858059","https://openalex.org/W2009994528","https://openalex.org/W2019624648","https://openalex.org/W2027065950","https://openalex.org/W2027139827","https://openalex.org/W2031757362","https://openalex.org/W2034133285","https://openalex.org/W2034372974","https://openalex.org/W2035602472","https://openalex.org/W2054010580","https://openalex.org/W2056975726","https://openalex.org/W2060718478","https://openalex.org/W2069165607","https://openalex.org/W2100141723","https://openalex.org/W2120468031","https://openalex.org/W2134036931","https://openalex.org/W2144730120","https://openalex.org/W2163414819","https://openalex.org/W2165961683","https://openalex.org/W2167530511"],"related_works":["https://openalex.org/W1148954706","https://openalex.org/W1528913684","https://openalex.org/W4282828727","https://openalex.org/W4388367611","https://openalex.org/W958315937","https://openalex.org/W1553613240","https://openalex.org/W21615084","https://openalex.org/W1967085530","https://openalex.org/W2372940580","https://openalex.org/W1986681646"],"abstract_inverted_index":{"Unlike":[0],"protein":[1],"folding,":[2],"the":[3,52,83,95,123,139,177,204,207,229],"process":[4],"by":[5],"which":[6,175],"a":[7,12,58,74,79,110,172,180],"large":[8,212],"RNA":[9,35],"molecule":[10],"adopts":[11],"functionally":[13],"active":[14],"conformation":[15],"remains":[16],"poorly":[17],"understood.":[18],"Chemical":[19],"mapping":[20],"techniques,":[21],"such":[22],"as":[23,36],"Hydroxyl":[24],"Radical":[25],"(\u00b7OH)":[26],"footprinting":[27],"report":[28],"on":[29,73,171],"local":[30],"structural":[31],"changes":[32],"in":[33,82,199],"an":[34],"it":[37],"folds":[38],"with":[39,118,158,211],"single":[40],"nucleotide":[41],"resolution.":[42],"The":[43],"analysis":[44],"and":[45,54,61],"interpretation":[46],"of":[47,57,85,141,206],"this":[48,69],"kinetic":[49,59,200,231],"data":[50,187,224],"requires":[51],"identification":[53],"subsequent":[55],"optimization":[56],"model":[60,201],"its":[62],"parameters.":[63],"We":[64],"detail":[65],"our":[66,129],"approach":[67,191],"to":[68,77,90,93,136,145,155,160,195,227,240],"problem,":[70],"specifically":[71],"focusing":[72],"novel":[75],"strategy":[76],"overcome":[78],"factorial":[80],"explosion":[81],"number":[84,140],"possible":[86],"models":[87,142],"that":[88,143],"need":[89,144,178],"be":[91,146,169],"tested":[92,147],"identify":[94],"best":[96],"fitting":[97],"model.":[98],"Previously,":[99],"smaller":[100],"systems":[101,117,157,166],"(less":[102],"than":[103],"three":[104,119],"intermediates)":[105],"were":[106],"computationally":[107,126],"tractable":[108],"using":[109,148],"distributed":[111,181],"computing":[112,182],"approach.":[113],"However,":[114],"for":[115,179,184,219],"larger":[116],"or":[120,233],"more":[121],"intermediates,":[122],"problem":[124],"became":[125],"intractable.":[127],"With":[128],"new":[130,190],"enumeration":[131],"strategy,":[132],"we":[133],"are":[134,238],"able":[135],"significantly":[137],"reduce":[138],"non-linear":[149],"least":[150],"squares":[151],"optimization,":[152],"allowing":[153],"us":[154,194],"study":[156,196],"up":[159],"five":[161],"intermediates.":[162],"Furthermore,":[163],"two":[164],"intermediate":[165],"can":[167],"now":[168],"analyzed":[170],"desktop":[173],"computer,":[174],"eliminates":[176],"solution":[183],"most":[185],"medium-sized":[186],"sets.":[188],"Our":[189],"also":[192],"allows":[193],"potential":[197],"degeneracy":[198],"selection,":[202],"elucidating":[203],"limits":[205],"method":[208],"when":[209],"working":[210],"systems.":[213],"This":[214],"work":[215],"establishes":[216],"clear":[217],"criteria":[218],"determining":[220],"if":[221,234],"experimental":[222,236],"\u00b7OH":[223],"is":[225],"sufficient":[226],"determine":[228],"underlying":[230],"model,":[232],"other":[235],"modalities":[237],"required":[239],"resolve":[241],"any":[242],"degeneracy.":[243]},"counts_by_year":[{"year":2016,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":3}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
