What Tools For Highly Detailed Analysis Of Point Mutation On A Known Structure

Question

[Wayne]

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!

[Michael]

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?

Answer 1

[Michael]

I have seen a presentation of Project Hope http://www2.cmbi.ru.nl/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.

Answer 2

[Chris Miller]

You might be interested in evolutionary trace: http://mammoth.bcm.tmc.edu/ETserver.html