{"id":"https://openalex.org/W2139895148","doi":"https://doi.org/10.1186/1471-2105-10-341","title":"Exploiting structural and topological information to improve prediction of RNA-protein binding sites","display_name":"Exploiting structural and topological information to improve prediction of RNA-protein binding sites","publication_year":2009,"publication_date":"2009-10-18","ids":{"openalex":"https://openalex.org/W2139895148","doi":"https://doi.org/10.1186/1471-2105-10-341","mag":"2139895148","pmid":"https://pubmed.ncbi.nlm.nih.gov/19835626"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-10-341","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-341","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-341","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":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-341","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5038112353","display_name":"Stefan Maetschke","orcid":"https://orcid.org/0000-0002-9540-1717"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Stefan R Maetschke","raw_affiliation_strings":["Institute for Molecular Bioscience, University of Queensland, QLD 4072, Australia. s.maetschke@imb.uq.edu.au","Institute for Molecular Bioscience, The University of Queensland, , Australia"],"affiliations":[{"raw_affiliation_string":"Institute for Molecular Bioscience, University of Queensland, QLD 4072, Australia. s.maetschke@imb.uq.edu.au","institution_ids":["https://openalex.org/I165143802"]},{"raw_affiliation_string":"Institute for Molecular Bioscience, The University of Queensland, , Australia","institution_ids":["https://openalex.org/I165143802"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100661224","display_name":"Zheng Yuan","orcid":"https://orcid.org/0000-0003-1254-0410"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Zheng Yuan","raw_affiliation_strings":["Institute for Molecular Bioscience and ARC Centre for Excellence in Bioinformatics, The University of Queensland, QLD, 4072, Australia","Institute for Molecular Bioscience and ARC Centre for Excellence in Bioinformatics, The University of Queensland, , Australia"],"affiliations":[{"raw_affiliation_string":"Institute for Molecular Bioscience and ARC Centre for Excellence in Bioinformatics, The University of Queensland, QLD, 4072, Australia","institution_ids":["https://openalex.org/I165143802"]},{"raw_affiliation_string":"Institute for Molecular Bioscience and ARC Centre for Excellence in Bioinformatics, The University of Queensland, , Australia","institution_ids":["https://openalex.org/I165143802"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5038112353"],"corresponding_institution_ids":["https://openalex.org/I165143802"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":2.5533,"has_fulltext":true,"cited_by_count":56,"citation_normalized_percentile":{"value":0.89733384,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"10","issue":"1","first_page":"341","last_page":"341"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9994000196456909,"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":0.9988999962806702,"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/betweenness-centrality","display_name":"Betweenness centrality","score":0.7975540161132812},{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"Support vector machine","score":0.6766993999481201},{"id":"https://openalex.org/keywords/naive-bayes-classifier","display_name":"Naive Bayes classifier","score":0.6073022484779358},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.606602668762207},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5243913531303406},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5204565525054932},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.48871350288391113},{"id":"https://openalex.org/keywords/bayes-theorem","display_name":"Bayes' theorem","score":0.47764861583709717},{"id":"https://openalex.org/keywords/matthews-correlation-coefficient","display_name":"Matthews correlation coefficient","score":0.43847382068634033},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.41396453976631165},{"id":"https://openalex.org/keywords/centrality","display_name":"Centrality","score":0.40179187059402466},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3923918604850769},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.37700027227401733},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3342018723487854},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.2782556414604187},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.26692497730255127},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.22441896796226501},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2104702591896057},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.10411763191223145}],"concepts":[{"id":"https://openalex.org/C117045392","wikidata":"https://www.wikidata.org/wiki/Q4899215","display_name":"Betweenness centrality","level":3,"score":0.7975540161132812},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.6766993999481201},{"id":"https://openalex.org/C52001869","wikidata":"https://www.wikidata.org/wiki/Q812530","display_name":"Naive Bayes classifier","level":3,"score":0.6073022484779358},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.606602668762207},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5243913531303406},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5204565525054932},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.48871350288391113},{"id":"https://openalex.org/C207201462","wikidata":"https://www.wikidata.org/wiki/Q182505","display_name":"Bayes' theorem","level":3,"score":0.47764861583709717},{"id":"https://openalex.org/C164085508","wikidata":"https://www.wikidata.org/wiki/Q4811327","display_name":"Matthews correlation coefficient","level":3,"score":0.43847382068634033},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.41396453976631165},{"id":"https://openalex.org/C53811970","wikidata":"https://www.wikidata.org/wiki/Q5062194","display_name":"Centrality","level":2,"score":0.40179187059402466},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3923918604850769},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.37700027227401733},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3342018723487854},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.2782556414604187},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.26692497730255127},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.22441896796226501},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2104702591896057},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.10411763191223145}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","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":"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":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-10-341","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-341","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-341","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:19835626","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19835626","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:doaj.org/article:190a7dd9f17447f3837444ef8fbbc46a","is_oa":true,"landing_page_url":"https://doaj.org/article/190a7dd9f17447f3837444ef8fbbc46a","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":"BMC Bioinformatics, Vol 10, Iss 1, p 341 (2009)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2774325","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2774325","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-10-341","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-341","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-341","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":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2139895148.pdf","grobid_xml":"https://content.openalex.org/works/W2139895148.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W1570448133","https://openalex.org/W1578097198","https://openalex.org/W1819481941","https://openalex.org/W1924414119","https://openalex.org/W1971894358","https://openalex.org/W1997828676","https://openalex.org/W2007922755","https://openalex.org/W2008708467","https://openalex.org/W2014731953","https://openalex.org/W2036887386","https://openalex.org/W2044775131","https://openalex.org/W2047928496","https://openalex.org/W2060683541","https://openalex.org/W2075220720","https://openalex.org/W2089621332","https://openalex.org/W2094148990","https://openalex.org/W2097694646","https://openalex.org/W2107432340","https://openalex.org/W2119493141","https://openalex.org/W2122854841","https://openalex.org/W2124974356","https://openalex.org/W2128393152","https://openalex.org/W2131322954","https://openalex.org/W2141149420","https://openalex.org/W2144476269","https://openalex.org/W2155653793","https://openalex.org/W2158698691","https://openalex.org/W2158714788","https://openalex.org/W2159291387","https://openalex.org/W2168055922","https://openalex.org/W2168272116","https://openalex.org/W2432517183","https://openalex.org/W2478668009","https://openalex.org/W3097169496","https://openalex.org/W4213345021"],"related_works":["https://openalex.org/W1973509935","https://openalex.org/W4389076551","https://openalex.org/W2097992793","https://openalex.org/W2107855069","https://openalex.org/W2611574733","https://openalex.org/W2241641394","https://openalex.org/W2140653560","https://openalex.org/W2348831795","https://openalex.org/W2514739320","https://openalex.org/W4312461432"],"abstract_inverted_index":{"Graph-theoretic":[0],"properties":[1],"of":[2],"residue":[3],"contact":[4],"maps":[5],"derived":[6],"from":[7],"protein":[8],"structures":[9],"such":[10],"as":[11],"betweenness-centrality":[12],"can":[13],"supplement":[14],"sequence":[15],"or":[16],"structure":[17],"features":[18],"to":[19,46],"improve":[20],"the":[21],"prediction":[22,49],"accuracy":[23],"for":[24,62],"binding":[25],"residues":[26],"in":[27],"RNA-protein":[28],"interactions.":[29],"While":[30],"Support":[31],"Vector":[32],"Machines":[33],"perform":[34],"better":[35],"on":[36],"this":[37],"task,":[38],"Na\u00efve":[39],"Bayes":[40],"classifiers":[41],"also":[42],"have":[43],"been":[44],"found":[45],"achieve":[47],"good":[48],"accuracies":[50],"but":[51],"require":[52],"much":[53],"less":[54],"training":[55],"time":[56],"and":[57],"are":[58],"an":[59],"attractive":[60],"choice":[61],"large":[63],"scale":[64],"predictions.":[65]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":7},{"year":2012,"cited_by_count":6}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}