Dear All,

I am doing few histone protein's SNP analysis.

I have used SIFT and Polyphen for my initial analysis. Now I would like predict its functional impact.

Can anyone please suggest me few tools or software for the prediction of the functional

effect of nsSNPs. Thank you
This is a good question. there are many other tools to investigate the functional effect of the SNPs.

In first instance you can model the SNPs into your protein structure of interest simple using the homology modeling (using mutate_model that you can get from the website of modeller) once you obtain your structure with the point mutation you can perform three type of analysis using three bioinformatics tools:

DSSP you can assign secondary structure both wild-type and to the variant protein and than you compare if there are a differences in the secondary structure(note that DSSP do not predict the secondary structure but only assign a possible structure)

HBPLUS you can use this tool to perform the analysis of the hydrogen bond to evaluate the pattern of hydrogen bond

NACCESS you can use this tools to evaluate the accessible areas of the molecule

If you have any questions can contact me