SNPeffect v2.0: a new step in investigating the molecular phenotypic effects of human non-synonymous SNPs.
paper
Cited
Public
Unavailable
- Authors
- Reumers, Joke; Maurer-Stroh, Sebastian; Schymkowitz, Joost; Rousseau, Frederic
- Year
- 2006
- Journal
- Bioinformatics (Oxford, England)
- PMID
- 16809394
- DOI
- 10.1093/bioinformatics/btl348
UNLABELLED: Single nucleotide polymorphisms (SNPs) constitute the most fundamental type of genetic variation in human populations. About 75 000 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. AVAILABILITY: SNPeffect can be accessed through http://snpeffect.vib.be.
No figures extracted from this document.
No chunks β full text not yet ingested.
No entities extracted from this document yet.
No uploaded files.
Not in any collection.
No citations found.
In this knowledge base
| Title | Year | PMID |
|---|---|---|
| SPOT: a web-based tool for using biological databases to prioritize SNPs after a genome-wide association study. | 2010 | 20529875 |
External
| Title | Authors | Journal | Year | Link |
|---|---|---|---|---|
| Predisposing deleterious variants in the cancer-associated human kinases in the global populations. | Khan SA et al. | β | 2024 | β |
| Variant Impact Predictor database (VIPdb), version 2: trends from three decades of genetic variant impact predictors. | Lin YJ et al. | β | 2024 | β |
| Integrative assessment of CIP2A overexpression and mutational effects in human malignancies identifies possible deleterious variants. | Tarek MM et al. | β | 2021 | β |
| Pred-MutHTP: Prediction of disease-causing and neutral mutations in human transmembrane proteins. | Kulandaisamy A et al. | β | 2020 | β |
| Ultra-High-Frequency Reprogramming of Individual Long-Term Hematopoietic Stem Cells Yields Low Somatic Variant Induced Pluripotent Stem Cells. | Wang K et al. | β | 2019 | β |
| Deletion of the miR172 target site in a TOE-type gene is a strong candidate variant for dominant double-flower trait in Rosaceae. | Gattolin S et al. | β | 2018 | β |
| Implication of OPRM1 A118G Polymorphism in Opioids Addicts in Pakistan: In vitro and In silico Analysis. | Ahmed M et al. | β | 2018 | β |
| Integrative genomics approaches validate PpYUC11-like as candidate gene for the stony hard trait in peach (P. persica L. Batsch). | Cirilli M et al. | β | 2018 | β |
| Vitamin D receptor (VDR) non-synonymous single nucleotide polymorphisms (nsSNPs) affect the calcitriol drug response - A theoretical insight. | Muthusamy K et al. | β | 2018 | β |
| Genetic dissection of Sharka disease tolerance in peach (P. persica L. Batsch). | Cirilli M et al. | β | 2017 | β |
| Prediction of a highly deleterious mutation E17K in AKT-1 gene: An <i>in silico</i> approach. | Khan I et al. | β | 2017 | β |
| Identification of type 2 diabetes subgroups through topological analysis of patient similarity. | Li L et al. | β | 2015 | β |
| Natural variability of minimotifs in 1092 people indicates that minimotifs are targets of evolution. | Lyon KF et al. | β | 2015 | β |
| Performance of In Silico Tools for the Evaluation of UGT1A1 Missense Variants. | Rodrigues C et al. | β | 2015 | β |
| Reconfiguring phosphorylation signaling by genetic polymorphisms affects cancer susceptibility. | Wang Y et al. | β | 2015 | β |
| Combined sequence and sequence-structure-based methods for analyzing RAAS gene SNPs: a computational approach. | Singh KhD et al. | β | 2014 | β |
| Comparative genomics of the pine pathogens and beetle symbionts in the genus Grosmannia. | Massoumi Alamouti S et al. | β | 2014 | β |
| Computational study of ADD1 gene polymorphism associated with hypertension. | Kundu A et al. | β | 2013 | β |
| Detection of regulatory SNPs in human genome using ChIP-seq ENCODE data. | Bryzgalov LO et al. | β | 2013 | β |
| Effect prediction of identified SNPs linked to fruit quality and chilling injury in peach [Prunus persica (L.) Batsch]. | MartΓnez-GarcΓa PJ et al. | β | 2013 | β |
| Extrapolating the effect of deleterious nsSNPs in the binding adaptability of flavopiridol with CDK7 protein: a molecular dynamics approach. | George Priya Doss C et al. | β | 2013 | β |
| Leucine to proline substitution by SNP at position 197 in Caspase-9 gene expression leads to neuroblastoma: a bioinformatics analysis. | Kundu A et al. | β | 2013 | β |
| Predicting the functional consequences of non-synonymous DNA sequence variants--evaluation of bioinformatics tools and development of a consensus strategy. | Frousios K et al. | β | 2013 | β |
| Predicting the impact of single-nucleotide polymorphisms in CDK2-flavopiridol complex by molecular dynamics analysis. | Nagasundaram N et al. | β | 2013 | β |
| A novel homozygous p.Arg527Leu LMNA mutation in two unrelated Egyptian families causes overlapping mandibuloacral dysplasia and progeria syndrome. | Al-Haggar M et al. | β | 2012 | β |
| Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation. | Gonzalez-Perez A et al. | β | 2012 | β |
| Interpretation of the consequences of mutations in protein kinases: combined use of bioinformatics and text mining. | Izarzugaza JM et al. | β | 2012 | β |
| Investigating the structural impacts of I64T and P311S mutations in APE1-DNA complex: a molecular dynamics approach. | Doss CG et al. | β | 2012 | β |
| regSNPs: a strategy for prioritizing regulatory single nucleotide substitutions. | Teng M et al. | β | 2012 | β |
| SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants. | De Baets G et al. | β | 2012 | β |
| Testing rare variants for association with diseases: a Bayesian marker selection approach. | Zhang L et al. | β | 2012 | β |
| AnnotQTL: a new tool to gather functional and comparative information on a genomic region. | Lecerf F et al. | β | 2011 | β |
| Compensated pathogenic deviations. | BareΕ‘iΔ A et al. | β | 2011 | β |
| Complement receptor 1 gene variants are associated with erythrocyte sedimentation rate. | Kullo IJ et al. | β | 2011 | β |
| Evaluation of the disease liability of CFTR variants. | Sosnay PR et al. | β | 2011 | β |
| Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel. | GonzΓ‘lez-PΓ©rez A et al. | β | 2011 | β |
| In silico analysis of single nucleotide polymorphism (SNPs) in human Ξ²-globin gene. | Alanazi M et al. | β | 2011 | β |
| In silico SNP analysis and bioinformatics tools: a review of the state of the art to aid drug discovery. | Mah JT et al. | β | 2011 | β |
| Meet me halfway: when genomics meets structural bioinformatics. | Gong S et al. | β | 2011 | β |
| Path to facilitate the prediction of functional amino acid substitutions in red blood cell disorders--a computational approach. | B R et al. | β | 2011 | β |
| A knowledge-based weighting framework to boost the power of genome-wide association studies. | Li MX et al. | β | 2010 | β |
| Alanine-to-threonine substitutions and amyloid diseases: butyrylcholinesterase as a case study. | Podoly E et al. | β | 2010 | β |
| Bioinformatic tools for identifying disease gene and SNP candidates. | Mooney SD et al. | β | 2010 | β |
| Computational analysis of missense mutations causing Snyder-Robinson syndrome. | Zhang Z et al. | β | 2010 | β |
| Computational identification and structural analysis of deleterious functional SNPs in MLL gene causing acute leukemia. | George Priya Doss C et al. | β | 2010 | β |
| FunctSNP: an R package to link SNPs to functional knowledge and dbAutoMaker: a suite of Perl scripts to build SNP databases. | Goodswen SJ et al. | β | 2010 | β |
| Improved detection of rare genetic variants for diseases. | Zhang L et al. | β | 2010 | β |
| Pharmacogenetics of drug metabolizing enzymes and transporters: effects on pharmacokinetics and pharmacodynamics of anticancer agents. | Lee NH | β | 2010 | β |
| PhosSNP for systematic analysis of genetic polymorphisms that influence protein phosphorylation. | Ren J et al. | β | 2010 | β |
| Prioritization of candidate SNPs in colon cancer using bioinformatics tools: an alternative approach for a cancer biologist. | George Priya Doss C et al. | β | 2010 | β |
| SPOT: a web-based tool for using biological databases to prioritize SNPs after a genome-wide association study. | Saccone SF et al. | β | 2010 | β |
| Association of MICA with rheumatoid arthritis independent of known HLA-DRB1 risk alleles in a family-based and a case control study. | Kirsten H et al. | β | 2009 | β |
| From SNPs to pathways: integration of functional effect of sequence variations on models of cell signalling pathways. | Bauer-Mehren A et al. | β | 2009 | β |
| Impact of single nucleotide polymorphisms in HBB gene causing haemoglobinopathies: in silico analysis. | George Priya Doss C et al. | β | 2009 | β |
| Next generation tools for the annotation of human SNPs. | Karchin R | β | 2009 | β |
| Pathogenic or not? And if so, then how? Studying the effects of missense mutations using bioinformatics methods. | Thusberg J et al. | β | 2009 | β |
| The SAAPdb web resource: a large-scale structural analysis of mutant proteins. | Hurst JM et al. | β | 2009 | β |
| A novel computational and structural analysis of nsSNPs in CFTR gene. | George Priya Doss C et al. | β | 2008 | β |
| Applications of computational algorithm tools to identify functional SNPs. | George Priya Doss C et al. | β | 2008 | β |
| Genetic variability in progranulin contributes to risk for clinically diagnosed Alzheimer disease. | Brouwers N et al. | β | 2008 | β |
| Genetic variability in the mitochondrial serine protease HTRA2 contributes to risk for Parkinson disease. | Bogaerts V et al. | β | 2008 | β |
| Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases. | Reumers J et al. | β | 2008 | β |
| A survey of genomic properties for the detection of regulatory polymorphisms. | Montgomery SB et al. | β | 2007 | β |
| DataBiNS: a BioMoby-based data-mining workflow for biological pathways and non-synonymous SNPs. | Song YC et al. | β | 2007 | β |
| PolyDoms: a whole genome database for the identification of non-synonymous coding SNPs with the potential to impact disease. | Jegga AG et al. | β | 2007 | β |