Question: How to determine if an amino acid is part of a-helix or B-sheet in pdb file
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gravatar for Mahmoud Ahmed
3.1 years ago by
Egypt,Cairo
Mahmoud Ahmed0 wrote:

Now I worked on "protein structure prediction" project and need to extract data from .pdb file , in this step I have to extract amino acid residue and determine if it was alpha-helix or beta-sheet ?

I had copy all content of the secondary structure section in pdb file but cant recognize my specified amino acid in it.

ADD COMMENTlink modified 3.1 years ago by Dan Gaston7.1k • written 3.1 years ago by Mahmoud Ahmed0
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gravatar for Ibrahim Tanyalcin
3.1 years ago by
Belgium
Ibrahim Tanyalcin930 wrote:

Dear Mahmoud,

You can download Swiss-Pdb Viewer (DeepView) at http://spdbv.vital-it.ch/ . You can open your pdb using it, and then go to Window(top right) and then select control panel. There on the leftmost side you will see S or H denoting strand or helix. You can also open the alignment window and see the same information in rectangular layout. I am pretty sure, you can do this by other commercially available pdb viewer packages as well.

Good luck,

ADD COMMENTlink written 3.1 years ago by Ibrahim Tanyalcin930
0
gravatar for Dan Gaston
3.1 years ago by
Dan Gaston7.1k
Canada
Dan Gaston7.1k wrote:

Typically the PDB file lists the first and last residues of a particular secondary structure element. So you would extract those from the various secondary structure lines and determine which, if any, your residue lies in based on those ranges. However, a given particular residue may lie in a loop region, and thus not be in any of the helix or sheet secondary structure designations.

PDB file format descriptions

ADD COMMENTlink written 3.1 years ago by Dan Gaston7.1k
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