Question: How to determine if an amino acid is part of a-helix or B-sheet in pdb file
gravatar for Mahmoud Ahmed
3.9 years ago by
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 3.9 years ago by DG7.1k • written 3.9 years ago by Mahmoud Ahmed0
gravatar for Ibrahim Tanyalcin
3.9 years ago by
Ibrahim Tanyalcin1.0k wrote:

Dear Mahmoud,

You can download Swiss-Pdb Viewer (DeepView) at . 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 3.9 years ago by Ibrahim Tanyalcin1.0k
gravatar for DG
3.9 years ago by
DG7.1k 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 3.9 years ago by DG7.1k
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