beta-sheet information from pdb file
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
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twisted_helix •
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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
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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.
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?
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.
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.