{"id":"https://openalex.org/W2103505761","doi":"https://doi.org/10.1093/nar/gkq361","title":"NAPS: a residue-level nucleic acid-binding prediction server","display_name":"NAPS: a residue-level nucleic acid-binding prediction server","publication_year":2010,"publication_date":"2010-05-15","ids":{"openalex":"https://openalex.org/W2103505761","doi":"https://doi.org/10.1093/nar/gkq361","mag":"2103505761","pmid":"https://pubmed.ncbi.nlm.nih.gov/20478832"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkq361","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkq361","pdf_url":null,"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":null,"license_id":null,"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://doi.org/10.1093/nar/gkq361","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5070956876","display_name":"Matthew B. Carson","orcid":"https://orcid.org/0000-0003-4105-9220"},"institutions":[{"id":"https://openalex.org/I39422238","display_name":"University of Illinois Chicago","ror":"https://ror.org/02mpq6x41","country_code":"US","type":"education","lineage":["https://openalex.org/I39422238"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Matthew B. Carson","raw_affiliation_strings":["Department of Bioengineering/Bioinformatics, University of Illinois at Chicago, Chicago, IL, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering/Bioinformatics, University of Illinois at Chicago, Chicago, IL, USA","institution_ids":["https://openalex.org/I39422238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020915161","display_name":"Robert Langlois","orcid":"https://orcid.org/0000-0003-1779-4786"},"institutions":[{"id":"https://openalex.org/I39422238","display_name":"University of Illinois Chicago","ror":"https://ror.org/02mpq6x41","country_code":"US","type":"education","lineage":["https://openalex.org/I39422238"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert Langlois","raw_affiliation_strings":["Department of Bioengineering/Bioinformatics, University of Illinois at Chicago, Chicago, IL, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering/Bioinformatics, University of Illinois at Chicago, Chicago, IL, USA","institution_ids":["https://openalex.org/I39422238"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100716955","display_name":"Hui L\u00fc","orcid":"https://orcid.org/0000-0001-8347-0830"},"institutions":[{"id":"https://openalex.org/I39422238","display_name":"University of Illinois Chicago","ror":"https://ror.org/02mpq6x41","country_code":"US","type":"education","lineage":["https://openalex.org/I39422238"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hui Lu","raw_affiliation_strings":["Department of Bioengineering/Bioinformatics, University of Illinois at Chicago, Chicago, IL, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering/Bioinformatics, University of Illinois at Chicago, Chicago, IL, USA","institution_ids":["https://openalex.org/I39422238"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5070956876"],"corresponding_institution_ids":["https://openalex.org/I39422238"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":2.7106,"has_fulltext":false,"cited_by_count":82,"citation_normalized_percentile":{"value":0.90312678,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"38","issue":"suppl_2","first_page":"W431","last_page":"W435"},"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9995999932289124,"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":0.9987000226974487,"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/nucleic-acid","display_name":"Nucleic acid","score":0.7908512353897095},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7207638025283813},{"id":"https://openalex.org/keywords/dna-binding-protein","display_name":"DNA-binding protein","score":0.5933011770248413},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5932561159133911},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.5915552377700806},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.5387635231018066},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.49055784940719604},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.4682909846305847},{"id":"https://openalex.org/keywords/rna-binding-protein","display_name":"RNA-binding protein","score":0.4613943099975586},{"id":"https://openalex.org/keywords/mutagenesis","display_name":"Mutagenesis","score":0.44611671566963196},{"id":"https://openalex.org/keywords/proteomics","display_name":"Proteomics","score":0.44236618280410767},{"id":"https://openalex.org/keywords/plasma-protein-binding","display_name":"Plasma protein binding","score":0.42709219455718994},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.19342026114463806},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.15103775262832642},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07041436433792114}],"concepts":[{"id":"https://openalex.org/C24107716","wikidata":"https://www.wikidata.org/wiki/Q123619","display_name":"Nucleic acid","level":2,"score":0.7908512353897095},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7207638025283813},{"id":"https://openalex.org/C94966510","wikidata":"https://www.wikidata.org/wiki/Q2252764","display_name":"DNA-binding protein","level":4,"score":0.5933011770248413},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5932561159133911},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5915552377700806},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.5387635231018066},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.49055784940719604},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4682909846305847},{"id":"https://openalex.org/C41282012","wikidata":"https://www.wikidata.org/wiki/Q3928341","display_name":"RNA-binding protein","level":4,"score":0.4613943099975586},{"id":"https://openalex.org/C16318435","wikidata":"https://www.wikidata.org/wiki/Q149299","display_name":"Mutagenesis","level":4,"score":0.44611671566963196},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.44236618280410767},{"id":"https://openalex.org/C51639874","wikidata":"https://www.wikidata.org/wiki/Q167149","display_name":"Plasma protein binding","level":2,"score":0.42709219455718994},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.19342026114463806},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.15103775262832642},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07041436433792114}],"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":"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":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","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":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"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":"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":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1093/nar/gkq361","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkq361","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:20478832","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20478832","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:CiteSeerX.psu:10.1.1.354.3560","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.354.3560","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/b9/d2/Nucleic_Acids_Res_2010_Jul_1_38(Web_Server_issue)_W431-W435.tar.gz","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.909.671","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.909.671","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/content/early/2010/05/16/nar.gkq361.full.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.917.587","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.917.587","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/content/38/suppl_2/W431.full-text-lowres.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.920.8850","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.920.8850","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/content/38/suppl_2/W431.full.pdf","raw_type":"text"},{"id":"pmh:oai:open-archive.highwire.org:nar:38/suppl_2/W431","is_oa":false,"landing_page_url":"http://nar.oxfordjournals.org/cgi/content/short/38/suppl_2/W431","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"},{"id":"pmh:oai:pubmedcentral.nih.gov:2896077","is_oa":true,"landing_page_url":"http://doi.org/10.1093/nar/gkq361","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":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkq361","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkq361","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W923169617","https://openalex.org/W1543773936","https://openalex.org/W1794828807","https://openalex.org/W1904417233","https://openalex.org/W1998518361","https://openalex.org/W2027364181","https://openalex.org/W2061307445","https://openalex.org/W2062606245","https://openalex.org/W2096223584","https://openalex.org/W2104707079","https://openalex.org/W2107255882","https://openalex.org/W2108880293","https://openalex.org/W2119493141","https://openalex.org/W2124974356","https://openalex.org/W2125055259","https://openalex.org/W2128533758","https://openalex.org/W2133141667","https://openalex.org/W2140514563","https://openalex.org/W2142261479","https://openalex.org/W2143210482","https://openalex.org/W2158714788","https://openalex.org/W2167287136","https://openalex.org/W2168272116","https://openalex.org/W2483545539","https://openalex.org/W2912934387","https://openalex.org/W4212883601","https://openalex.org/W6676739762","https://openalex.org/W6684730997"],"related_works":["https://openalex.org/W4385345739","https://openalex.org/W2515311730","https://openalex.org/W1985254234","https://openalex.org/W2499154798","https://openalex.org/W2065704027","https://openalex.org/W1982819881","https://openalex.org/W1963992374","https://openalex.org/W2009673058","https://openalex.org/W4365811105","https://openalex.org/W2103375140"],"abstract_inverted_index":{"Nucleic":[0],"acid-binding":[1],"proteins":[2,17],"are":[3],"involved":[4,25,76],"in":[5,26,38,61,77,87],"a":[6,67],"great":[7],"number":[8],"of":[9,22,31,42,72,113],"cellular":[10],"processes.":[11],"Understanding":[12],"the":[13,20,39,57,70,91,107],"mechanisms":[14],"underlying":[15],"these":[16,62],"first":[18],"requires":[19],"identification":[21,71],"specific":[23],"residues":[24,33,60,75],"nucleic":[27],"acid":[28,74],"binding.":[29],"Prediction":[30],"NA-binding":[32,43],"can":[34,46],"provide":[35],"practical":[36],"assistance":[37],"functional":[40],"annotation":[41],"proteins.":[44,63],"Predictions":[45],"also":[47],"be":[48],"used":[49,86],"to":[50,56],"expedite":[51],"mutagenesis":[52],"experiments,":[53],"guiding":[54],"researchers":[55],"correct":[58],"binding":[59],"Here,":[64],"we":[65],"present":[66],"method":[68,85],"for":[69],"amino":[73],"DNA-":[78],"and":[79,97],"RNA-binding":[80,108],"using":[81],"sequence-based":[82],"attributes.":[83],"The":[84,115],"this":[88],"work":[89],"combines":[90],"C4.5":[92],"algorithm":[93],"with":[94],"bootstrap":[95],"aggregation":[96],"cost-sensitive":[98],"learning.":[99],"Our":[100],"DNA-binding":[101],"model":[102,109],"achieved":[103],"79.1%":[104],"accuracy,":[105],"while":[106],"reached":[110],"an":[111],"accuracy":[112],"73.2%.":[114],"NAPS":[116],"web":[117],"server":[118],"is":[119],"freely":[120],"available":[121],"at":[122],"http://proteomics.bioengr.uic.edu/NAPS.":[123]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":8},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":8},{"year":2015,"cited_by_count":11},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":4}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}