{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,2]],"date-time":"2026-07-02T11:07:53Z","timestamp":1782990473689,"version":"3.54.5"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1738,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Many existing databases annotate experimentally characterized single nucleotide polymorphisms (SNPs). Each non-synonymous SNP (nsSNP) changes one amino acid in the gene product (single amino acid substitution;SAAS). This change can either affect protein function or be neutral in that respect. Most polymorphisms lack experimental annotation of their functional impact. Here, we introduce SNPdbe\u2014SNP database of effects, with predictions of computationally annotated functional impacts of SNPs. Database entries represent nsSNPs in dbSNP and 1000 Genomes collection, as well as variants from UniProt and PMD. SAASs come from &amp;gt;2600 organisms; \u2018human\u2019 being the most prevalent. The impact of each SAAS on protein function is predicted using the SNAP and SIFT algorithms and augmented with experimentally derived function\/structure information and disease associations from PMD, OMIM and UniProt. SNPdbe is consistently updated and easily augmented with new sources of information. The database is available as an MySQL dump and via a web front end that allows searches with any combination of organism names, sequences and mutation IDs.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/www.rostlab.org\/services\/snpdbe<\/jats:p>\n               <jats:p>Contact: \u00a0schaefer@rostlab.org; snpdbe@rostlab.org<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr705","type":"journal-article","created":{"date-parts":[[2012,1,1]],"date-time":"2012-01-01T01:24:24Z","timestamp":1325381064000},"page":"601-602","source":"Crossref","is-referenced-by-count":43,"title":["SNPdbe: constructing an nsSNP functional impacts database"],"prefix":"10.1093","volume":"28","author":[{"given":"Christian","family":"Schaefer","sequence":"first","affiliation":[{"name":"1 Technische Universitaet Muenchen, Bioinformatics \u2013 I12, Informatik, Boltzmannstrasse 3, 2Technische Universitaet Muenchen Graduate School of Information Science in Health (GSISH), Boltzmannstrasse 11, 85748 Garching, Germany and 3Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901, USA"},{"name":"1 Technische Universitaet Muenchen, Bioinformatics \u2013 I12, Informatik, Boltzmannstrasse 3, 2Technische Universitaet Muenchen Graduate School of Information Science in Health (GSISH), Boltzmannstrasse 11, 85748 Garching, Germany and 3Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alice","family":"Meier","sequence":"additional","affiliation":[{"name":"1 Technische Universitaet Muenchen, Bioinformatics \u2013 I12, Informatik, Boltzmannstrasse 3, 2Technische Universitaet Muenchen Graduate School of Information Science in Health (GSISH), Boltzmannstrasse 11, 85748 Garching, Germany and 3Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Burkhard","family":"Rost","sequence":"additional","affiliation":[{"name":"1 Technische Universitaet Muenchen, Bioinformatics \u2013 I12, Informatik, Boltzmannstrasse 3, 2Technische Universitaet Muenchen Graduate School of Information Science in Health (GSISH), Boltzmannstrasse 11, 85748 Garching, Germany and 3Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901, USA"},{"name":"1 Technische Universitaet Muenchen, Bioinformatics \u2013 I12, Informatik, Boltzmannstrasse 3, 2Technische Universitaet Muenchen Graduate School of Information Science in Health (GSISH), Boltzmannstrasse 11, 85748 Garching, Germany and 3Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yana","family":"Bromberg","sequence":"additional","affiliation":[{"name":"1 Technische Universitaet Muenchen, Bioinformatics \u2013 I12, Informatik, Boltzmannstrasse 3, 2Technische Universitaet Muenchen Graduate School of Information Science in Health (GSISH), Boltzmannstrasse 11, 85748 Garching, Germany and 3Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2011,12,30]]},"reference":[{"key":"2023012512192264500_B1","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.1038\/nature09534","article-title":"A map of human genome variation from population-scale 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Res."},{"key":"2023012512192264500_B5","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2023012512192264500_B6","doi-asserted-by":"crossref","first-page":"3823","DOI":"10.1093\/nar\/gkm238","article-title":"SNAP: predict effect of non-synonymous polymorphisms on function","volume":"35","author":"Bromberg","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2023012512192264500_B7","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1093\/bioinformatics\/btn653","article-title":"SNPnexus: a web database for functional annotation of newly discovered and public domain single nucleotide polymorphisms","volume":"25","author":"Chelala","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012512192264500_B8","doi-asserted-by":"crossref","first-page":"D700","DOI":"10.1093\/nar\/gkl826","article-title":"PolyDoms: a whole genome database for the identification of non-synonymous coding SNPs with the potential to impact disease","volume":"35","author":"Jegga","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2023012512192264500_B9","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1093\/nar\/27.1.355","article-title":"The Protein Mutant Database","volume":"27","author":"Kawabata","year":"1999","journal-title":"Nucleic Acids Res."},{"key":"2023012512192264500_B10","doi-asserted-by":"crossref","first-page":"1858","DOI":"10.1093\/bioinformatics\/btg241","article-title":"MutDB: annotating human variation with functionally relevant data","volume":"19","author":"Mooney","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012512192264500_B11","doi-asserted-by":"crossref","first-page":"863","DOI":"10.1101\/gr.176601","article-title":"Predicting deleterious amino acid substitutions","volume":"11","author":"Ng","year":"2001","journal-title":"Genome Res."},{"key":"2023012512192264500_B12","doi-asserted-by":"crossref","first-page":"D61","DOI":"10.1093\/nar\/gkl842","article-title":"NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins","volume":"35","author":"Pruitt","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2023012512192264500_B13","doi-asserted-by":"crossref","first-page":"e118","DOI":"10.1093\/nar\/gkr407","article-title":"Predicting the functional impact of protein mutations: application to cancer genomics","volume":"39","author":"Reva","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023012512192264500_B14","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1093\/nar\/29.1.308","article-title":"dbSNP: the NCBI database of genetic variation","volume":"29","author":"Sherry","year":"2001","journal-title":"Nucleic Acids 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