{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,29]],"date-time":"2026-03-29T12:22:18Z","timestamp":1774786938405,"version":"3.50.1"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"17","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Single nucleotide polymorphisms (SNPs) constitute the most fundamental type of genetic variation in human populations. About 75\u2009000 of these reported variations cause an amino acid change in the translated protein. An important goal in genomic research is to understand how this variability affects protein function, and whether or not particular SNPs are associated to disease susceptibility. Accordingly, the SNPeffect database uses sequence- and structure-based bioinformatics tools to predict the effect of non-synonymous SNPs on the molecular phenotype of proteins. SNPeffect analyses the effect of SNPs on three categories of functional properties: (1) structural and thermodynamic properties affecting protein dynamics and stability (2) the integrity of functional and binding sites and (3) changes in posttranslational processing and cellular localization of proteins. The search interface of the database can be used to search specifically for polymorphisms that are predicted to cause a change in one of these properties. Now based on the Ensembl human databases, the SNPeffect database has been remodeled to better fit an automatically updatable structure. The current edition holds the molecular phenotype of 74 567 nsSNPs in 23 426 proteins.<\/jats:p>\n               <jats:p>Availability: SNPeffect can be accessed through<\/jats:p>\n               <jats:p>Supplementary Material: Statistics on the contents of the database, figures on the workflow used to create the database and information on the used sources and tools is available at .<\/jats:p>\n               <jats:p>Contact: \u00a0joost.schymkowitz@vub.ac.be or frederic.rousseau@vub.ac.be<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl348","type":"journal-article","created":{"date-parts":[[2006,6,30]],"date-time":"2006-06-30T14:27:07Z","timestamp":1151677627000},"page":"2183-2185","source":"Crossref","is-referenced-by-count":70,"title":["SNPeffect v2.0: a new step in investigating the molecular phenotypic effects of human non-synonymous SNPs"],"prefix":"10.1093","volume":"22","author":[{"given":"Joke","family":"Reumers","sequence":"first","affiliation":[{"name":"Switch Laboratory, Flanders Interuniversity Institute of Biotechnology, Vrije Universiteit Brussel \u00a0 Pleinlaan 2, Brussels, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sebastian","family":"Maurer-Stroh","sequence":"additional","affiliation":[{"name":"Switch Laboratory, Flanders Interuniversity Institute of Biotechnology, Vrije Universiteit Brussel \u00a0 Pleinlaan 2, Brussels, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joost","family":"Schymkowitz","sequence":"additional","affiliation":[{"name":"Switch Laboratory, Flanders Interuniversity Institute of Biotechnology, Vrije Universiteit Brussel \u00a0 Pleinlaan 2, Brussels, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Frederic","family":"Rousseau","sequence":"additional","affiliation":[{"name":"Switch Laboratory, Flanders Interuniversity Institute of Biotechnology, Vrije Universiteit Brussel \u00a0 Pleinlaan 2, Brussels, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2006,6,29]]},"reference":[{"key":"2023012409132497200_b1","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1126\/science.3018930","article-title":"In vivo half-life of a protein is a function of its amino-terminal residue","volume":"234","author":"Bachmair","year":"1986","journal-title":"Science"},{"key":"2023012409132497200_b2","doi-asserted-by":"crossref","first-page":"D556","DOI":"10.1093\/nar\/gkj133","article-title":"Ensembl 2006","volume":"34","author":"Birney","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023012409132497200_b3","doi-asserted-by":"crossref","first-page":"W501","DOI":"10.1093\/nar\/gki476","article-title":"PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes","volume":"33","author":"Conde","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012409132497200_b4","doi-asserted-by":"crossref","first-page":"921","DOI":"10.1126\/science.8346443","article-title":"Gene dose of apolipoprotein E type 4 allele and the risk of Alzheimer's disease in late onset families","volume":"261","author":"Corder","year":"1993","journal-title":"Science"},{"key":"2023012409132497200_b5","article-title":"The pymol molecular graphics system","author":"DeLano","year":"2004"},{"key":"2023012409132497200_b6","doi-asserted-by":"crossref","first-page":"D233","DOI":"10.1093\/nar\/gki057","article-title":"The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema","volume":"33","author":"Deshpande","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012409132497200_b7","doi-asserted-by":"crossref","first-page":"3631","DOI":"10.1093\/nar\/gkg537","article-title":"Prediction of lipid posttranslational modifications and localization signals from protein sequences: big-pi, nmt and pts1","volume":"31","author":"Eisenhaber","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023012409132497200_b8","doi-asserted-by":"crossref","first-page":"1302","DOI":"10.1038\/nbt1012","article-title":"Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins","volume":"22","author":"Fernandez-Escamilla","year":"2004","journal-title":"Nat. Biotechnol."},{"key":"2023012409132497200_b9","doi-asserted-by":"crossref","first-page":"370","DOI":"10.1093\/nar\/27.1.370","article-title":"O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins","volume":"27","author":"Gupta","year":"1999","journal-title":"Nucleic Acids Res."},{"key":"2023012409132497200_b10","doi-asserted-by":"crossref","first-page":"1027","DOI":"10.1016\/j.jmb.2004.03.016","article-title":"A combined transmembrane topology and signal peptide prediction method","volume":"338","author":"Kall","year":"2004","journal-title":"J. Mol. Biol."},{"key":"2023012409132497200_b11","doi-asserted-by":"crossref","first-page":"D230","DOI":"10.1093\/nar\/gkh008","article-title":"The SWISS-MODEL repository of annotated three-dimensional protein structure homology models","volume":"32","author":"Kopp","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023012409132497200_b12","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1093\/nar\/27.1.237","article-title":"PhosphoBase, a database of phosphorylation sites: release 2.0","volume":"29","author":"Kreegipuu","year":"1999","journal-title":"Nucleic Acids Res."},{"key":"2023012409132497200_b13","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1073\/pnas.2634884100","article-title":"Sequence determinants of amyloid fibril formation","volume":"101","author":"L\u00f3pez de la Paz","year":"2004","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012409132497200_b14","doi-asserted-by":"crossref","first-page":"R55","DOI":"10.1186\/gb-2005-6-6-r55","article-title":"Refinement and prediction of protein prenylation motifs","volume":"6","author":"Maurer-Stroh","year":"2005","journal-title":"Genome Biol."},{"key":"2023012409132497200_b15","first-page":"34","article-title":"PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization","volume":"24","author":"Nakai","year":"1999","journal-title":"TIBS"},{"key":"2023012409132497200_b16","doi-asserted-by":"crossref","first-page":"D129","DOI":"10.1093\/nar\/gkh028","article-title":"The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data","volume":"32","author":"Porter","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023012409132497200_b17","doi-asserted-by":"crossref","first-page":"D527","DOI":"10.1093\/nar\/gki086","article-title":"SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs","volume":"33","author":"Reumers","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012409132497200_b18","doi-asserted-by":"crossref","first-page":"584","DOI":"10.1006\/jmbi.1993.1413","article-title":"Prediction of protein secondary structure at better than 70-percent accuracy","volume":"232","author":"Rost","year":"1993","journal-title":"J. Mol. Biol."},{"key":"2023012409132497200_b19","doi-asserted-by":"crossref","first-page":"1037","DOI":"10.1016\/j.jmb.2005.11.035","article-title":"How evolutionary pressure against protein aggregation shaped chaperone specificity","volume":"355","author":"Rousseau","year":"1986","journal-title":"J. Mol. Biol."},{"key":"2023012409132497200_b20","doi-asserted-by":"crossref","first-page":"W382","DOI":"10.1093\/nar\/gki387","article-title":"The FoldX web server: an online force field","volume":"33","author":"Schymkowitz","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012409132497200_b21","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 Res."},{"key":"2023012409132497200_b22","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1038\/ng1733","article-title":"A SNP in the ABCC11 gene is the determinant of human earwax type","volume":"38","author":"Yoshiura","year":"2006","journal-title":"Nat. Genet."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/17\/2183\/48839616\/bioinformatics_22_17_2183.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/17\/2183\/48839616\/bioinformatics_22_17_2183.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,24]],"date-time":"2023-01-24T09:51:45Z","timestamp":1674553905000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/22\/17\/2183\/273711"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,6,29]]},"references-count":22,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2006,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btl348","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2006,9,1]]},"published":{"date-parts":[[2006,6,29]]}}}