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Protein structure modeling for enzymes with point mutations


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#1 Talesta

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Posted 14 May 2013 - 04:58 AM

Hello,
I have an accurate 3D model of my enzyme. I'm looking for some software to predict/analyze the structural changes associated with single point mutations that I introduce in the molecule.
Any ideas? I'd be grateful for any possible suggestions.

#2 GNANA

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Posted 15 May 2013 - 02:18 AM

I am not an expert here, but seen ppl using 'SWISS MODEL server' http://swissmodel.ex....org/workspace/ to predict 3D structure. i am not sure whether this tool could also be used to analyse single amino acid changes, but worth giving a try.

Beside this, my suggestion is to check the degree of conservation of the aminoacid through SIFT analysis http://sift.jcvi.org/ , may be this would give you an idea about the atlered AA is tolerated or damaging in respect to its function.
I would prefer being perfectionist rather than a passionist in Research.

I always had an alternate hypothesis....

#3 Talesta

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Posted 15 May 2013 - 04:18 AM

GNANA, thank you very much! Especially for the SIFT: I never heard of it before. It’ll make my work so much easier!
I'll try SWISS MODEL server. I also did some googling of my own. The Modeller (salilab.org/modeller/‎) software seems to be a popular tool for my purpose, but SWISS MODEL seems to be much easier to handle. I wonder if a more complicated tool is worth an effort.
Thank you once again!

#4 GNANA

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Posted 15 May 2013 - 04:36 AM

you are welcome, i dnt think you would hav got much to do when you use SWISS modeling server, just upload your query AA seq and you ll get the pdb in your workspace. better predict in two or three different tools. and another tip i can give you is to use a good 'pdb file' visualizing software, other than the conventional 'Rasmol' , i would recomend you to use this one http://www.cgl.ucsf....a/download.html, which is good especially when you compare protein 3D strs (like WT and mutated in your case) simultaneously.

good luck...
I would prefer being perfectionist rather than a passionist in Research.

I always had an alternate hypothesis....




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