Question: What is the best/mostcommon approach to model the effect of missense SNP on protein structure?
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gravatar for english.server
6 months ago by
Germany
english.server160 wrote:

What is the best approach to model the 3D structure of a mutant protein if we already have the 3d structure of the original protein? Is modeller suited to this work or does it depend on the location of mutation (ie loop vs core)?

Thank you in advance

snp protein structure • 292 views
ADD COMMENTlink modified 8 weeks ago by jgreener100 • written 6 months ago by english.server160
3
gravatar for Kevin Blighe
6 months ago by
Kevin Blighe46k
Kevin Blighe46k wrote:

Technically, the following make their predictions based on protein sequence and/or structure

However, you probably want one of the modeling tools from the Protein Model Portal. There, you can merely input your amino acid sequence and it will model the predicted structure for you. I know of at least one clinical geneticist who uses this to see how mutations from live patient data could affect protein structure. I believe the modelers return a PDB file

I list these along with other tools, here:

Kevin

ADD COMMENTlink written 6 months ago by Kevin Blighe46k
1

Thank you indeed very much. Much helpful tools you've suggested in the linked post.

ADD REPLYlink written 6 months ago by english.server160
1
gravatar for jgreener
8 weeks ago by
jgreener100
United Kingdom
jgreener100 wrote:

The recently-released Missense3D provides a nice interface to explore this problem.

ADD COMMENTlink written 8 weeks ago by jgreener100

Hey, can you please make a new 'Tool' post about this, and write a description (if you are the developer)? Then it will receive more hits from search engines.

ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by Kevin Blighe46k

Sorry, I am not the developer, it was made in my PhD lab but after I left. I don't have enough knowledge of the tool to write a Tool post.

ADD REPLYlink written 8 weeks ago by jgreener100

Sure thing - no wworries

ADD REPLYlink written 8 weeks ago by Kevin Blighe46k
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