How To Evaluate The Effect That A Snp Has On The Structure And Function Of The Protein?

Question

[rt.cgen]

I am working on SNP and I have narrowed down my search to 1 SNP which I believe is most damaging to the structure and function of the protein. I want to test this hypothesis (the hypothesis being that this particular mutation caused by SNP would be most damaging to the native protein structure) with as many ways possible. I have already tested my hypothesis by carrying out Molecular Dynamics Simulation (MDS) and Bayesian theorem and both of the fore mentioned methods corroborate my finding.

I would really appreciate if you can suggest some more ways to test my hypothesis, I am looking for computational and mathematical methods only. Thanks in Advance, your help is highly appreciated.

[Giovanni M Dall'Olio]

How did you identify this SNP? You should distinguish whether your SNP is the actual SNP that cause the phenotype, or just a tag SNPs that is close to the real variant that causes the disease. If you have identified the SNP from GWAS analysis or similar method, the latter case is the most probable.

[rt.cgen]

It is not a tagSNP as I downloaded all the ns SNP associated with the gene from dbSNP and analyzed the loss of structural and functional properties that SNP would have on protein.

[Zhilong Jia]

@Rohit . Any update? BTW, which tools you use to implement Molecular Dynamics Simulation? Thank you.

Answer 1

[Jorge Amigo]

there are many tools out there you may use for functional prediction: SIFT, PolyPhen2, PhyloP, snpEff,...

one that seems to perform really nice by combining several indexes is Condel

[rt.cgen]

@Jorge Amigo - I think I did not make myself clear(or you did not get my query), I have already mentioned that I narrowed down my search to 1 SNP using but not limited to the servers that you have mentioned.I now need to test my hypothesis and I have already done so by using MDS and Bayesian. I am looking for more ways to test my hypothesis.