beta-sheet information from pdb file

Question

[twisted_helix]

hello, i am a student working on quantitatively finding secondary structure of protein. I would like to know how do i fine the number of amino acid that correspond to beta-sheets in a .pdb file. this information will help me to compute the percentage of beta-sheets in the structure.

your inputs will be of great value to me.

Thank you

[Pallab Bhowmick]

Try to use http://swift.cmbi.ru.nl/gv/dssp/ and it will provide you with the secondary structure environment of each amino acid in the structure. If the secondary structure is "H", it is a helix; if it is "E" it is a beta sheet; a "C" consider it coil.

[twisted_helix]

thanks pb for this valuable information. I am exploring the link.

I thought i only have to read the textual information under SHEET and that gives information. I am trying to get the information in my python code. Am i on the right track?

[Pallab Bhowmick]

Yes, you can write your own python script to get the result. For more information please visit their webpage and you will get more idea.

[microfuge]

Hi, Uniprot also provides this information in a convenient tabular format. For example for this entry http://www.uniprot.org/uniprot/Q00534 check structure-tab -> secondary-structure-> show details. Could easily be parsed out from the uniprot flatfile for a large scale analysis.

Answer 1

[Persistent LABS]

Hi

You can use iCAPS (http://irdp.ncl.res.in/CompStabAna.html). This tool can be used to compare secondary structure content across 100 protein structures simultaneously. It also supports comparative analysis of other structural features too.

Thanks

Persistent LABS