Hello everybody,
I am working in a wet lab on characterizing a protein sequence that do not have a PDB id, so no structure, I would like to predit the effect of single mutation in the primary sequence on the hedrophobic region of the sequence (i mean effect on the structure), what are the tools that I have to use and what is the process that I have to follow to do that ?
Thank you
2 answers
Wow! Didn't know about that or ProTherm. Added to my toolset!
But, watch for this: http://www.ncbi.nlm.nih.gov/pubmed/19561092. These methods aren't as good as reported. Homology modeling still outperforms. The homology modeling/SDM/Andante combination seems to stand as the best option for now.
Not to toot my own horn, but is sounds like http://www.cmbi.ru.nl/hope/home well suits your needs, provided homologs are available to build a homology model.
Just enter your sequence & mutation, wait for the model to be build, and you'll get a human readable report detailing the effects on the protein structure.
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Is it a totally new protein? No homologs? No similar fold? If it has homologs/similars your case has a solution. Otherwise, this is a very very hazy situation.
just to refine the problem better, how have you identified the mutation? Is it by linkage (the mutation is associated with the mutation, but not necessarily the cause) or by other methods? Moreover, is it a SNP or a more extended mutation?