Question: What Tools For Highly Detailed Analysis Of Point Mutation On A Known Structure
gravatar for Wayne
6.8 years ago by
United States
Wayne1.0k wrote:

What tools would one recommend for assessing the functional impact of a Non synonymous mutation on a known crystal structure. My method so far is to completely digest the literature available, and then use Modeller or I-Tasser to predict ab initio changes and then try put the pieces together. I need to be able to say things like " Amino acid 1 can no longer Hbond amino acid 5, or disulfide bridge between amino acids 5 and 10 is no longer feasible..... ligand binding pocket A is predicted to have lower binding potential.

I know these are not easy questions to answer, and certainly not definitive, but I think a reliable prediction of the structural changes caused by a mutant is a good place to start. Any suggestions would be very helpful!

ADD COMMENTlink modified 5.2 years ago by Biostar ♦♦ 20 • written 6.8 years ago by Wayne1.0k

You have asked a very similar question before: How to create a reliable structural homology model of a missense mutation? and accepted the answer, this question looks almost like a duplicate. The answer to your first question also fits for this question as it lists a set of tools to predict the effect of an amino acid change given a known structure. Can you explain, what has changed?

ADD REPLYlink modified 6.8 years ago • written 6.8 years ago by Michael Dondrup47k
gravatar for Michael Dondrup
6.8 years ago by
Bergen, Norway
Michael Dondrup47k wrote:

I have seen a presentation of Project Hope lately (server is temporarily down, check later) in a course, it looks like a good point to start. It will generate sentences very similar to your example on disulfide bridges.

ADD COMMENTlink written 6.8 years ago by Michael Dondrup47k
gravatar for Chris Miller
6.8 years ago by
Chris Miller21k
Washington University in St. Louis, MO
Chris Miller21k wrote:

You might be interested in evolutionary trace:

ADD COMMENTlink written 6.8 years ago by Chris Miller21k
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