Question: Predicting Effect Of Single Mutation On Protein Structure
5
gravatar for Patrick
9.1 years ago by
Patrick50
Patrick50 wrote:

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

mutation protein structure • 6.9k views
ADD COMMENTlink modified 9.0 years ago by Tim320 • written 9.1 years ago by Patrick50

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.

ADD REPLYlink written 9.1 years ago by Jarretinha3.3k

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?

ADD REPLYlink written 9.1 years ago by Giovanni M Dall'Olio27k
2
gravatar for Dataminer
9.1 years ago by
Dataminer2.7k
Netherlands
Dataminer2.7k wrote:

If you have protein sequence, you can use mutant-I.

let me know, if you have more questions.

ADD COMMENTlink modified 6 months ago by RamRS26k • written 9.1 years ago by Dataminer2.7k

Thanks for the tool that's great !

ADD REPLYlink written 9.1 years ago by Patrick50

Wow! Didn't know about that or ProTherm. Added to my toolset!

ADD REPLYlink written 9.1 years ago by Jarretinha3.3k

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.

ADD REPLYlink written 9.1 years ago by Jarretinha3.3k
2
gravatar for Tim
9.1 years ago by
Tim320
Nijmegen, the Netherlands
Tim320 wrote:

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.

ADD COMMENTlink written 9.1 years ago by Tim320

Thank you this is a cool tool in fact !

ADD REPLYlink written 9.1 years ago by Patrick50
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