{"id":"https://openalex.org/W2134425918","doi":"https://doi.org/10.1093/nar/gks513","title":"NASSAM: a server to search for and annotate tertiary interactions and motifs in three-dimensional structures of complex RNA molecules","display_name":"NASSAM: a server to search for and annotate tertiary interactions and motifs in three-dimensional structures of complex RNA molecules","publication_year":2012,"publication_date":"2012-05-31","ids":{"openalex":"https://openalex.org/W2134425918","doi":"https://doi.org/10.1093/nar/gks513","mag":"2134425918","pmid":"https://pubmed.ncbi.nlm.nih.gov/22661578"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gks513","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gks513","pdf_url":"https://academic.oup.com/nar/article-pdf/40/W1/W35/4928880/gks513.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/40/W1/W35/4928880/gks513.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5048356979","display_name":"Hazrina Yusof Hamdani","orcid":"https://orcid.org/0000-0003-3973-9921"},"institutions":[{"id":"https://openalex.org/I885383172","display_name":"National University of Malaysia","ror":"https://ror.org/00bw8d226","country_code":"MY","type":"education","lineage":["https://openalex.org/I885383172"]}],"countries":["MY"],"is_corresponding":false,"raw_author_name":"H. Y. Hamdani","raw_affiliation_strings":["School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Malaysia","School of Biosciences and Biotechnology, Faculty of Science & Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Malaysia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Malaysia","institution_ids":["https://openalex.org/I885383172"]},{"raw_affiliation_string":"School of Biosciences and Biotechnology, Faculty of Science & Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Malaysia","institution_ids":["https://openalex.org/I885383172"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006208366","display_name":"Sri Devan Appasamy","orcid":"https://orcid.org/0000-0001-6609-3535"},"institutions":[{"id":"https://openalex.org/I885383172","display_name":"National University of Malaysia","ror":"https://ror.org/00bw8d226","country_code":"MY","type":"education","lineage":["https://openalex.org/I885383172"]},{"id":"https://openalex.org/I91136226","display_name":"University of Sheffield","ror":"https://ror.org/05krs5044","country_code":"GB","type":"education","lineage":["https://openalex.org/I91136226"]}],"countries":["GB","MY"],"is_corresponding":false,"raw_author_name":"S. D. Appasamy","raw_affiliation_strings":["School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Malaysia, 2 Information School and 3 Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, UK","National University of Malaysia, Bangi, Malaysia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Malaysia, 2 Information School and 3 Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, UK","institution_ids":["https://openalex.org/I91136226"]},{"raw_affiliation_string":"National University of Malaysia, Bangi, Malaysia","institution_ids":["https://openalex.org/I885383172"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019392883","display_name":"Peter Willett","orcid":"https://orcid.org/0000-0001-8443-5586"},"institutions":[{"id":"https://openalex.org/I885383172","display_name":"National University of Malaysia","ror":"https://ror.org/00bw8d226","country_code":"MY","type":"education","lineage":["https://openalex.org/I885383172"]},{"id":"https://openalex.org/I91136226","display_name":"University of Sheffield","ror":"https://ror.org/05krs5044","country_code":"GB","type":"education","lineage":["https://openalex.org/I91136226"]}],"countries":["GB","MY"],"is_corresponding":false,"raw_author_name":"P. Willett","raw_affiliation_strings":["School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Malaysia, 2 Information School and 3 Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, UK","National University of Malaysia, Bangi, Malaysia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Malaysia, 2 Information School and 3 Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, UK","institution_ids":["https://openalex.org/I91136226"]},{"raw_affiliation_string":"National University of Malaysia, Bangi, Malaysia","institution_ids":["https://openalex.org/I885383172"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108693804","display_name":"P.J. Artymiuk","orcid":null},"institutions":[{"id":"https://openalex.org/I885383172","display_name":"National University of Malaysia","ror":"https://ror.org/00bw8d226","country_code":"MY","type":"education","lineage":["https://openalex.org/I885383172"]},{"id":"https://openalex.org/I91136226","display_name":"University of Sheffield","ror":"https://ror.org/05krs5044","country_code":"GB","type":"education","lineage":["https://openalex.org/I91136226"]}],"countries":["GB","MY"],"is_corresponding":true,"raw_author_name":"P. J. Artymiuk","raw_affiliation_strings":["School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Malaysia, 2 Information School and 3 Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, UK","National University of Malaysia, Bangi, Malaysia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Malaysia, 2 Information School and 3 Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, UK","institution_ids":["https://openalex.org/I91136226"]},{"raw_affiliation_string":"National University of Malaysia, Bangi, Malaysia","institution_ids":["https://openalex.org/I885383172"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070763648","display_name":"Mohd Firdaus\u2010Raih","orcid":"https://orcid.org/0000-0003-4275-4663"},"institutions":[{"id":"https://openalex.org/I885383172","display_name":"National University of Malaysia","ror":"https://ror.org/00bw8d226","country_code":"MY","type":"education","lineage":["https://openalex.org/I885383172"]},{"id":"https://openalex.org/I91136226","display_name":"University of Sheffield","ror":"https://ror.org/05krs5044","country_code":"GB","type":"education","lineage":["https://openalex.org/I91136226"]}],"countries":["GB","MY"],"is_corresponding":false,"raw_author_name":"M. Firdaus-Raih","raw_affiliation_strings":["School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Malaysia, 2 Information School and 3 Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, UK","National University of Malaysia, Bangi, Malaysia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Malaysia, 2 Information School and 3 Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, UK","institution_ids":["https://openalex.org/I91136226"]},{"raw_affiliation_string":"National University of Malaysia, Bangi, Malaysia","institution_ids":["https://openalex.org/I885383172"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5108693804"],"corresponding_institution_ids":["https://openalex.org/I885383172","https://openalex.org/I91136226"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":1.1048,"has_fulltext":true,"cited_by_count":25,"citation_normalized_percentile":{"value":0.7638902,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"40","issue":"W1","first_page":"W35","last_page":"W41"},"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":0.9993000030517578,"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":0.9990000128746033,"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/biology","display_name":"Biology","score":0.7184504866600037},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.5567034482955933},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5408334136009216},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5358688831329346},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4852306842803955},{"id":"https://openalex.org/keywords/login","display_name":"Login","score":0.4812600314617157},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4569126069545746},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.45278874039649963},{"id":"https://openalex.org/keywords/base","display_name":"Base (topology)","score":0.4298058748245239},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3469225764274597},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.32528799772262573},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19696250557899475},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.14981341361999512},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.13566547632217407},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11684951186180115},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.10542765259742737}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7184504866600037},{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.5567034482955933},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5408334136009216},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5358688831329346},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4852306842803955},{"id":"https://openalex.org/C113324615","wikidata":"https://www.wikidata.org/wiki/Q472302","display_name":"Login","level":2,"score":0.4812600314617157},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4569126069545746},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.45278874039649963},{"id":"https://openalex.org/C42058472","wikidata":"https://www.wikidata.org/wiki/Q810214","display_name":"Base (topology)","level":2,"score":0.4298058748245239},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3469225764274597},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.32528799772262573},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19696250557899475},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.14981341361999512},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.13566547632217407},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11684951186180115},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.10542765259742737},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"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/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.0}],"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":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":"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":"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":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/nar/gks513","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gks513","pdf_url":"https://academic.oup.com/nar/article-pdf/40/W1/W35/4928880/gks513.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:22661578","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22661578","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:eprints.whiterose.ac.uk:74879","is_oa":false,"landing_page_url":"http://eprints.whiterose.ac.uk/74879/1/W35.full.pdf","pdf_url":"http://eprints.whiterose.ac.uk/74879/1/W35.full.pdf","source":{"id":"https://openalex.org/S4306400854","display_name":"White Rose Research Online (University of Leeds, The University of Sheffield, University of York)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2800616092","host_organization_name":"White Rose University Consortium","host_organization_lineage":["https://openalex.org/I2800616092"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:europepmc.org:2409768","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3394293","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:open-archive.highwire.org:nar:40/W1/W35","is_oa":false,"landing_page_url":"http://nar.oxfordjournals.org/cgi/content/short/40/W1/W35","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":{"id":"doi:10.1093/nar/gks513","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gks513","pdf_url":"https://academic.oup.com/nar/article-pdf/40/W1/W35/4928880/gks513.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321709","display_name":"Ministry of Higher Education, Malaysia","ror":"https://ror.org/05mcs2t73"},{"id":"https://openalex.org/F4320322699","display_name":"Universiti Kebangsaan Malaysia","ror":"https://ror.org/00bw8d226"},{"id":"https://openalex.org/F4320322757","display_name":"Universiti Sains Malaysia","ror":"https://ror.org/02rgb2k63"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2134425918.pdf","grobid_xml":"https://content.openalex.org/works/W2134425918.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W1971957619","https://openalex.org/W1983534198","https://openalex.org/W1992105696","https://openalex.org/W1995554116","https://openalex.org/W2006640104","https://openalex.org/W2007615447","https://openalex.org/W2009555898","https://openalex.org/W2013902881","https://openalex.org/W2018838912","https://openalex.org/W2020657839","https://openalex.org/W2040447892","https://openalex.org/W2055317682","https://openalex.org/W2055688390","https://openalex.org/W2060167034","https://openalex.org/W2070166301","https://openalex.org/W2076317271","https://openalex.org/W2087101377","https://openalex.org/W2090007205","https://openalex.org/W2090278190","https://openalex.org/W2101449937","https://openalex.org/W2106246926","https://openalex.org/W2106746359","https://openalex.org/W2120418017","https://openalex.org/W2126359798","https://openalex.org/W2130479394","https://openalex.org/W2131575287","https://openalex.org/W2132129663","https://openalex.org/W2158073100","https://openalex.org/W2167338363","https://openalex.org/W2172206224","https://openalex.org/W3041019241"],"related_works":["https://openalex.org/W2035334116","https://openalex.org/W2145118195","https://openalex.org/W2013211627","https://openalex.org/W2032140021","https://openalex.org/W4220987767","https://openalex.org/W2104334314","https://openalex.org/W2948436713","https://openalex.org/W2903628238","https://openalex.org/W3208481717","https://openalex.org/W2888012743"],"abstract_inverted_index":{"Similarities":[0],"in":[1,19,110,121],"the":[2,22,50,58,74,77,81,84,122],"3D":[3,24,43,95],"patterns":[4,44,109,116],"of":[5,21,45,57,106],"RNA":[6,23],"base":[7,46,107],"interactions":[8],"or":[9,124],"arrangements":[10,47],"can":[11,40,66,100],"provide":[12],"insights":[13],"into":[14],"their":[15],"functions":[16],"and":[17,31,129],"roles":[18],"stabilization":[20,131],"structure.":[25],"Nucleic":[26],"Acids":[27],"Search":[28],"for":[29,42,90],"Substructures":[30],"Motifs":[32],"(NASSAM)":[33],"is":[34,136],"a":[35,64,70,111],"graph":[36,72],"theoretical":[37],"program":[38,135],"that":[39,117,125],"search":[41],"by":[48],"representing":[49],"bases":[51],"as":[52,63,69],"pseudo-atoms.":[53],"The":[54,87,133],"geometric":[55],"relationship":[56],"pseudo-atoms":[59,75],"to":[60,103,114],"each":[61],"other":[62],"pattern":[65],"be":[67,101],"represented":[68],"labeled":[71],"where":[73],"are":[76,83,92],"graph's":[78],"nodes":[79],"while":[80],"edges":[82],"inter-pseudo-atomic":[85],"distances.":[86],"input":[88],"files":[89],"NASSAM":[91,134],"PDB":[93],"formatted":[94],"coordinates.":[96],"This":[97],"web":[98],"server":[99],"used":[102],"identify":[104],"matches":[105],"arrangement":[108],"query":[112],"structure":[113],"annotated":[115],"have":[118,126],"been":[119],"reported":[120],"literature":[123],"possible":[127],"functional":[128],"structural":[130],"implications.":[132],"freely":[137],"accessible":[138],"without":[139],"any":[140],"login":[141],"requirement":[142],"at":[143],"http://mfrlab.org/grafss/nassam/.":[144]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":2}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
