SNPeffect v2.0: a new step in investigating the molecular phenotypic effects of human non-synonymous SNPs

@article{Reumers2006SNPeffectVA,
  title={SNPeffect v2.0: a new step in investigating the molecular phenotypic effects of human non-synonymous SNPs},
  author={Joke Reumers and Sebastian Maurer-Stroh and Joost Schymkowitz and Frederic Rousseau},
  journal={Bioinformatics},
  year={2006},
  volume={22 17},
  pages={
          2183-5
        }
}
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… 

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References

SHOWING 1-10 OF 27 REFERENCES

SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs

The current release of SNPeffect incorporates data on protein stability, integrity of functional sites, protein phosphorylation and glycosylation, subcellular localization, protein turnover rates, protein aggregation, amyloidosis and chaperone interaction.

PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes

PupasView is the first resource that integrates phenotypic effects caused by SNPs at both the translational and the transcriptional level and will be of much help in studies of multifactorial disorders, where the use of functional SNPs will increase the sensitivity of the identification of the genes responsible for the disease.

Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins

The results confirm the model of intermolecular β-sheet formation as a widespread underlying mechanism of protein aggregation and opens the door to a fully automated, sequence-based design strategy to improve the aggregation properties of proteins of scientific or industrial interest.

A SNP in the ABCC11 gene is the determinant of human earwax type

It is shown that a SNP, 538G → A (rs17822931), in the ABCC11 gene is responsible for determination of earwax type, and this is the first example of DNA polymorphism determining a visible genetic trait.

The FoldX web server: an online force field

The core functionality of FoldX, namely the calculation of the free energy of a macromolecule based on its high-resolution 3D structure, is now publicly available through a web server at FoldX.

Prediction of lipid posttranslational modifications and localization signals from protein sequences: big-, NMT and PTS1

The myristoyl transferase (NMT) predictor recognizes glycine N-myristoylation sites (at the N-terminus and for fragments after processing) of higher eukaryotes (including their viruses and fungi), and the PTS1 signal predictor finds proteins with a C- terminus appropriate for peroxisomal import (for metazoa and fungi).

Prediction of protein secondary structure at better than 70% accuracy.

A two-layered feed-forward neural network is trained on a non-redundant data base to predict the secondary structure of water-soluble proteins with a new key aspect is the use of evolutionary information in the form of multiple sequence alignments that are used as input in place of single sequences.

Refinement and prediction of protein prenylation motifs

Prenylation Prediction Suite can predict partially overlapping substrate specificities, which is of medical importance in the case of understanding cellular action of FT inhibitors as anticancer and anti-parasite agents.

The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema

The Research Collaboratory for Structural Bioinformatics (RCSB) has completely redesigned its resource for the distribution and query of 3D structure data, expanding the functionality of the existing site by providing structure data in greater detail and uniformity, improved query and enhanced analysis tools.