What is the best/mostcommon approach to model the effect of missense SNP on protein structure?

Question

[english.server]

What is the best approach to model the 3D structure of a mutant protein if we already have the 3d structure of the original protein? Is modeller suited to this work or does it depend on the location of mutation (ie loop vs core)?

Thank you in advance

Answer 1

[Kevin Blighe]

Technically, the following make their predictions based on protein sequence and/or structure

• PolyPhen-2
• LS-SNP/PDB
• SNPeffect 4.0

However, you probably want one of the modeling tools from the Protein Model Portal. There, you can merely input your amino acid sequence and it will model the predicted structure for you. I know of at least one clinical geneticist who uses this to see how mutations from live patient data could affect protein structure. I believe the modelers return a PDB file

I list these along with other tools, here:

• A: How to choose good tools for identifying functional SNPs?
• A: pathogenicity predictors of cancer mutations

Kevin

[english.server]

Thank you indeed very much. Much helpful tools you've suggested in the linked post.

Answer 2

[jgreener]

The recently-released Missense3D provides a nice interface to explore this problem.

[Kevin Blighe]

Hey, can you please make a new 'Tool' post about this, and write a description (if you are the developer)? Then it will receive more hits from search engines.

[jgreener]

Sorry, I am not the developer, it was made in my PhD lab but after I left. I don't have enough knowledge of the tool to write a Tool post.

[Kevin Blighe]

Sure thing - no wworries