{"id":"https://openalex.org/W2068462102","doi":"https://doi.org/10.1145/2147805.2147832","title":"Predicting folding pathways between RNA conformational structures guided by RNA stacks","display_name":"Predicting folding pathways between RNA conformational structures guided by RNA stacks","publication_year":2011,"publication_date":"2011-08-01","ids":{"openalex":"https://openalex.org/W2068462102","doi":"https://doi.org/10.1145/2147805.2147832","mag":"2068462102"},"language":"en","primary_location":{"id":"doi:10.1145/2147805.2147832","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2147805.2147832","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100409803","display_name":"Yuan Li","orcid":"https://orcid.org/0000-0002-3287-1199"},"institutions":[{"id":"https://openalex.org/I106165777","display_name":"University of Central Florida","ror":"https://ror.org/036nfer12","country_code":"US","type":"education","lineage":["https://openalex.org/I106165777"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yuan Li","raw_affiliation_strings":["University of Central Florida, Orlando, FL","University of Central, Florida, Orlando, FL#TAB#"],"affiliations":[{"raw_affiliation_string":"University of Central Florida, Orlando, FL","institution_ids":["https://openalex.org/I106165777"]},{"raw_affiliation_string":"University of Central, Florida, Orlando, FL#TAB#","institution_ids":["https://openalex.org/I106165777"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100768909","display_name":"Shaojie Zhang","orcid":"https://orcid.org/0000-0002-4051-5549"},"institutions":[{"id":"https://openalex.org/I106165777","display_name":"University of Central Florida","ror":"https://ror.org/036nfer12","country_code":"US","type":"education","lineage":["https://openalex.org/I106165777"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shaojie Zhang","raw_affiliation_strings":["University of Central Florida, Orlando, FL","University of Central, Florida, Orlando, FL#TAB#"],"affiliations":[{"raw_affiliation_string":"University of Central Florida, Orlando, FL","institution_ids":["https://openalex.org/I106165777"]},{"raw_affiliation_string":"University of Central, Florida, Orlando, FL#TAB#","institution_ids":["https://openalex.org/I106165777"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5100409803"],"corresponding_institution_ids":["https://openalex.org/I106165777"],"apc_list":null,"apc_paid":null,"fwci":0.1303,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.52279325,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"245","last_page":"253"},"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9980000257492065,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9969000220298767,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/folding","display_name":"Folding (DSP implementation)","score":0.7900099754333496},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.6019009351730347},{"id":"https://openalex.org/keywords/energy-landscape","display_name":"Energy landscape","score":0.5904014706611633},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5703567862510681},{"id":"https://openalex.org/keywords/heuristic","display_name":"Heuristic","score":0.5559480786323547},{"id":"https://openalex.org/keywords/local-optimum","display_name":"Local optimum","score":0.48354053497314453},{"id":"https://openalex.org/keywords/protein-folding","display_name":"Protein folding","score":0.45586374402046204},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3993913531303406},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.36282414197921753},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3289080262184143},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.27253949642181396},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1833258867263794},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.16951489448547363},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.14380738139152527},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11189854145050049},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.07253110408782959}],"concepts":[{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.7900099754333496},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.6019009351730347},{"id":"https://openalex.org/C119621388","wikidata":"https://www.wikidata.org/wiki/Q5377166","display_name":"Energy landscape","level":2,"score":0.5904014706611633},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5703567862510681},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.5559480786323547},{"id":"https://openalex.org/C141934464","wikidata":"https://www.wikidata.org/wiki/Q3305386","display_name":"Local optimum","level":2,"score":0.48354053497314453},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.45586374402046204},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3993913531303406},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.36282414197921753},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3289080262184143},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.27253949642181396},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1833258867263794},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.16951489448547363},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.14380738139152527},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11189854145050049},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.07253110408782959},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/2147805.2147832","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2147805.2147832","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.8700000047683716,"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":41,"referenced_works":["https://openalex.org/W44682325","https://openalex.org/W56340226","https://openalex.org/W107776513","https://openalex.org/W189083333","https://openalex.org/W1524617288","https://openalex.org/W1828328674","https://openalex.org/W1977083306","https://openalex.org/W1982463627","https://openalex.org/W1987385830","https://openalex.org/W1995612793","https://openalex.org/W2000191287","https://openalex.org/W2009818318","https://openalex.org/W2016916568","https://openalex.org/W2018483756","https://openalex.org/W2019890308","https://openalex.org/W2024417034","https://openalex.org/W2033706116","https://openalex.org/W2042332384","https://openalex.org/W2054931730","https://openalex.org/W2073380384","https://openalex.org/W2085235576","https://openalex.org/W2096883982","https://openalex.org/W2103250001","https://openalex.org/W2106769579","https://openalex.org/W2114001343","https://openalex.org/W2117431427","https://openalex.org/W2124162379","https://openalex.org/W2124191447","https://openalex.org/W2126244322","https://openalex.org/W2128737924","https://openalex.org/W2143726250","https://openalex.org/W2146297415","https://openalex.org/W2146346646","https://openalex.org/W2157052506","https://openalex.org/W2158863640","https://openalex.org/W2162310257","https://openalex.org/W2164408046","https://openalex.org/W2170576426","https://openalex.org/W3122583070","https://openalex.org/W4238678686","https://openalex.org/W6678670499"],"related_works":["https://openalex.org/W2186061937","https://openalex.org/W2476476683","https://openalex.org/W2789914061","https://openalex.org/W2907629594","https://openalex.org/W2113188411","https://openalex.org/W2083241011","https://openalex.org/W1919653159","https://openalex.org/W1974862140","https://openalex.org/W2467603891","https://openalex.org/W2081866413"],"abstract_inverted_index":{"In":[0],"this":[1],"paper,":[2],"we":[3,67],"propose":[4,68],"a":[5,20],"new":[6],"algorithm":[7,70],"for":[8],"predicting":[9],"low":[10],"energy":[11,56,121],"barrier":[12,122],"folding":[13,32,76,90,123],"pathways":[14,33,77,91,124],"between":[15,125],"conformational":[16,129],"secondary":[17,126],"structures":[18,39,127],"of":[19,31,37,54,75,83,89,96,112,128,144],"single":[21],"RNA":[22,55,84,97],"molecule.":[23],"Most":[24],"existing":[25,134],"heuristic":[26,135],"algorithms":[27,136],"guide":[28],"the":[29,41,45,50,73,79,87,102,133],"construction":[30,74,88],"by":[34,92],"free":[35],"energies":[36],"intermediate":[38],"in":[40,63,137],"next":[42],"move":[43],"during":[44],"folding.":[46],"However":[47],"due":[48],"to":[49,109,118],"size":[51],"and":[52,81,105,131,146],"ruggedness":[53],"landscape,":[57],"energy-guided":[58],"search":[59,103],"can":[60,99],"become":[61],"trapped":[62],"local":[64,113],"optima.":[65,114],"Here,":[66],"an":[69],"that":[71],"guides":[72],"through":[78],"formation":[80],"destruction":[82],"stacks.":[85],"Guiding":[86],"coarse":[93],"grained":[94],"movements":[95],"stacks":[98],"help":[100],"reduce":[101],"space":[104],"make":[106],"it":[107],"easier":[108],"jump":[110],"out":[111],"RNAEAPath":[115,145],"is":[116],"able":[117],"find":[119],"lower":[120],"switches":[130],"outperforms":[132],"most":[138],"test":[139],"cases.":[140],"The":[141],"source":[142],"code":[143],"associated":[147],"supplementary":[148],"data":[149],"are":[150],"available":[151],"at":[152],"http://genome.ucf.edu/RNAEAPath.":[153]},"counts_by_year":[{"year":2014,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
