{"id":"https://openalex.org/W2122951823","doi":"https://doi.org/10.1093/bioinformatics/btv369","title":"FoldNucleus: web server for the prediction of RNA and protein folding nuclei from their 3D structures","display_name":"FoldNucleus: web server for the prediction of RNA and protein folding nuclei from their 3D structures","publication_year":2015,"publication_date":"2015-06-22","ids":{"openalex":"https://openalex.org/W2122951823","doi":"https://doi.org/10.1093/bioinformatics/btv369","mag":"2122951823","pmid":"https://pubmed.ncbi.nlm.nih.gov/26104744"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv369","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv369","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5028096134","display_name":"Leonid Pereyaslavets","orcid":"https://orcid.org/0000-0001-5410-2318"},"institutions":[{"id":"https://openalex.org/I4210137602","display_name":"Institute of Protein Research","ror":"https://ror.org/0489f0s93","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210129690","https://openalex.org/I4210137602"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Leonid B. Pereyaslavets","raw_affiliation_strings":["Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia","institution_ids":["https://openalex.org/I4210137602"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023228709","display_name":"Igor V. Sokolovsky","orcid":null},"institutions":[{"id":"https://openalex.org/I4210137602","display_name":"Institute of Protein Research","ror":"https://ror.org/0489f0s93","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210129690","https://openalex.org/I4210137602"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Igor V. Sokolovsky","raw_affiliation_strings":["Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia","institution_ids":["https://openalex.org/I4210137602"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023828983","display_name":"Oxana V. Galzitskaya","orcid":"https://orcid.org/0000-0002-3962-1520"},"institutions":[{"id":"https://openalex.org/I4210137602","display_name":"Institute of Protein Research","ror":"https://ror.org/0489f0s93","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210129690","https://openalex.org/I4210137602"]}],"countries":["RU"],"is_corresponding":true,"raw_author_name":"Oxana V. Galzitskaya","raw_affiliation_strings":["Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia","institution_ids":["https://openalex.org/I4210137602"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5023828983"],"corresponding_institution_ids":["https://openalex.org/I4210137602"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.5912,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.6876129,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"31","issue":"20","first_page":"3374","last_page":"3376"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9042999744415283,"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":0.9042999744415283,"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":0.01730000041425228,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.012000000104308128,"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/ribozyme","display_name":"Ribozyme","score":0.7788410782814026},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.7503509521484375},{"id":"https://openalex.org/keywords/folding","display_name":"Folding (DSP implementation)","score":0.676998496055603},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.5471987128257751},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4792380630970001},{"id":"https://openalex.org/keywords/protein-folding","display_name":"Protein folding","score":0.46240049600601196},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.4369580149650574},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4227634072303772},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.412834107875824},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3907366693019867},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3192059397697449},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.21892499923706055},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.1293235421180725},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.09131357073783875},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.07078918814659119}],"concepts":[{"id":"https://openalex.org/C76346623","wikidata":"https://www.wikidata.org/wiki/Q205858","display_name":"Ribozyme","level":4,"score":0.7788410782814026},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.7503509521484375},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.676998496055603},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.5471987128257751},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4792380630970001},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.46240049600601196},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.4369580149650574},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4227634072303772},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.412834107875824},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3907366693019867},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3192059397697449},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.21892499923706055},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.1293235421180725},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.09131357073783875},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.07078918814659119},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein 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":"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":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":3,"locations":[{"id":"doi:10.1093/bioinformatics/btv369","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv369","pdf_url":null,"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:26104744","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26104744","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:open-archive.highwire.org:bioinfo:31/20/3374","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/31/20/3374","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":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320324099","display_name":"Russian Science Foundation","ror":"https://ror.org/03y2gwe85"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":10,"referenced_works":["https://openalex.org/W113688923","https://openalex.org/W1970680503","https://openalex.org/W2078960884","https://openalex.org/W2083969154","https://openalex.org/W2112032866","https://openalex.org/W2120468031","https://openalex.org/W2134036931","https://openalex.org/W2157467256","https://openalex.org/W6604582531","https://openalex.org/W6670349568"],"related_works":["https://openalex.org/W2260493136","https://openalex.org/W2113188411","https://openalex.org/W4210423528","https://openalex.org/W2976965029","https://openalex.org/W2382178265","https://openalex.org/W2055827177","https://openalex.org/W2072666835","https://openalex.org/W4248706500","https://openalex.org/W2939859775","https://openalex.org/W2103379028"],"abstract_inverted_index":{"MOTIVATION:":[0],"To":[1],"gain":[2],"insight":[3],"into":[4],"how":[5],"biopolymers":[6],"fold":[7],"as":[8,10,66,68],"quickly":[9],"they":[11,69],"do,":[12],"it":[13,39],"is":[14,40],"useful":[15],"to":[16,42],"determine":[17,79],"which":[18,82],"structural":[19],"elements":[20,83],"limit":[21,87],"the":[22,44,85,88],"rate":[23],"of":[24,84,94],"RNA/protein":[25],"folding.":[26],"SUMMARY:":[27],"We":[28],"have":[29],"created":[30],"a":[31],"new":[32],"web":[33],"server,":[34,38],"FoldNucleus.":[35],"Using":[36],"this":[37],"possible":[41],"calculate":[43],"folding":[45,89],"nucleus":[46],"for":[47,59,91,102],"RNA":[48],"molecules":[49,61],"with":[50,62,110],"known":[51,63],"3D":[52,64],"structures-including":[53],"pseudoknots,":[54],"tRNAs,":[55],"hairpins":[56],"and":[57,80,96,108],"ribozymes-and":[58],"protein":[60,97],"structures,":[65],"long":[67],"are":[70],"smaller":[71],"than":[72],"200":[73],"amino":[74],"acid":[75],"residues.":[76],"Researchers":[77],"can":[78,105],"understand":[81],"structure":[86],"process":[90],"various":[92],"types":[93],"RNAs":[95],"molecules.":[98],"Experimental":[99],"\u0424":[100],"values":[101],"21":[103],"proteins":[104],"be":[106],"found":[107],"compared":[109],"those":[111],"determined":[112],"by":[113],"our":[114],"method:":[115],"http://bioinfo.protres.ru/resources/phi_values.htm.":[116],"AVAILABILITY":[117],"AND":[118],"IMPLEMENTATION:":[119],"http://bioinfo.protres.ru/foldnucleus/.":[120],"CONTACT:":[121],"ogalzit@vega.protres.ru.":[122]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2026-06-23T06:36:01.041984","created_date":"2025-10-10T00:00:00"}
