Protein Structure comparison, WT and Mutant

Question

[sv91707]

Hi all,

Does anyone know any tools or softwares, which I can use to compare effect of protein structure - of a validated mutation (missense), between WT and mutant ?

Answer 1

[otterad]

If you are looking to compare your two sequences, you could use ITASSER server (http://zhanglab.ccmb.med.umich.edu/I-TASSER/). You will need a academic email address and can only submit one job at a time, or if you're confident, download the suite (upon approval of an academic license)

It is great for protein structure prediction but is only a prediction, so your mutation could change the structure but take it with a pinch of salt.

Edit: There is also PANTHER cSNP scoring, if you mutation is a single SNP (http://www.pantherdb.org/tools/csnpScoreForm.jsp), it estimates if a single SNP has a functional effect on the function of the protein. I've never used it but have come across it a few times

Answer 2

[Carlo Yague]

There is also PoPMusic (Prediction of Protein Mutant Stability Changes) that tells you how a mutation is going to affect the stability of a protein :

A web server that predicts the thermodynamic stability changes caused by single site mutations in proteins, using a linear combination of statistical potentials whose coefficients depend on the solvent accessibility of the mutated residue. PoPMuSiC presents good prediction performances (correlation coefficient of 0.8 between predicted and measured stability changes, in cross validation, after exclusion of 10% outliers). It is moreover very fast, allowing the prediction of the stability changes resulting from all possible mutations in a medium size protein in less than a minute. This unique functionality is user-friendly implemented in PoPMuSiC and is particularly easy to exploit.