Question: Tool for visualizing proteins based on amino-acid structure?
1
gravatar for sviatoslav.kendall
4.8 years ago by
United States
sviatoslav.kendall480 wrote:

I'm working on a gene discovery project and in which we've established a list of candidate genes that have mutations in evolutionarily conserved locations in subjects suffering from the disease. At this point, we want to compare structural impact of the mutations with the wild-type but many of our candidate genes do not have entries on Protopedia (http://proteopedia.org/wiki/index.php/Main_Page), let alone the mutations found in our samples.

 

Anyone know of some good tools for visualizing proteins based on their primary structure alone? 

sequence proteomics gene • 1.3k views
ADD COMMENTlink modified 4.8 years ago by João Rodrigues2.5k • written 4.8 years ago by sviatoslav.kendall480
1
gravatar for João Rodrigues
4.8 years ago by
João Rodrigues2.5k
Stanford University, U
João Rodrigues2.5k wrote:

Did you try looking for structures in the RCSB PDB? You should only need _one_ structure, and then evaluate the impact of the mutations based on this single structure by analysing the chemical environment of the amino acid being mutated. You can also try to do some in silico mutagenesis and evaluate the stability of the mutant by molecular dynamics for example, but for large scale study this is impractical..

ADD COMMENTlink written 4.8 years ago by João Rodrigues2.5k

Thanks; I'll check this out. Only have 8 genes to look at so it shouldn't be too bad

ADD REPLYlink written 4.8 years ago by sviatoslav.kendall480
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