My software notes

April 8, 2011

Find salt bridges quickly using VMD

Filed under: pymol/ molmol — kpwu @ 12:58 pm
Tags: ,

My colleagues asked me to know if they can use PyMol to quickly find information of salt bridges in their working proteins. It seems there is no simple pymol script to do such purpose (at least I can’t find it).

I tried writing a shell scripts to extract coordinates from all negative (Glu, Asp) and positive (Lys, Arg) charged residues and calculate the distances to know if there are any salt bridges in the protein. Before I finish that coding work, I found that VMD actually provide such analysis tool! Good job VMD!.

Here is a snapshot and using protein EnvZ (PDB code: 1BXD) as an example. The output of analysis is shown in the terminal window.

Definition of salt bridge can be found at Wikipedia.

VMD can be downloaded at VMD official site.

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8 Comments »

  1. I was hoping you could help us analyze a peptide we are trying to make. We suspect there are some troublesome salt bridges with. Could you run your software and let us know? The sequence is,

    VYIQYQGFRVQLESMKKLSDLEAQWAPSPRLQAQSLLPAVCHHPALPQDLQPVCASQEASSIFKTLRTIANDD

    Comment by Rick Coughlin — August 9, 2011 @ 3:35 am | Reply

  2. Rick, as I know, to analyze whether your interesting protein/peptide has salt bridge, you need to have atomic coordinate(s) in hands first. I have no ideas how to predict the salt bridge based on primary sequence. Perhaps this is a good research project for bioinformatic persons.

    Comment by kpwu — August 9, 2011 @ 5:18 pm | Reply

  3. just curious…
    what was the distance you choose to define a salt bridge?

    Comment by Murpholino Peligro — March 21, 2012 @ 10:38 pm | Reply

  4. I don’t make my own “cut-off”, I simply use VMD to get a list of salt bridges. Please check VMD’s online info at http://www.ks.uiuc.edu/Research/vmd/plugins/saltbr/

    Quote from above link “A salt bridge is considered to be formed if the distance between any of the oxygen atoms of acidic residues and the nitrogen atoms of basic residues are within the cut-off distance (default 3.2 Angstroms) in at least one frame. “

    Comment by kpwu — March 22, 2012 @ 12:20 am | Reply

  5. Hi! you can also use the tool “‘Timeline”and Calculate Salt Bridge. This way it shows you a graph with the behavior of the salt bridge in time.

    Comment by Mariana — August 23, 2012 @ 2:09 pm | Reply

  6. you can use SBION for this purpose..http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3974244/

    Comment by panther — July 8, 2014 @ 12:55 pm | Reply

  7. The improved version of SBION i.e SBION2 can be downloaded from http://sourceforge.net/projects/sbion2/

    Comment by Parth — March 24, 2015 @ 8:14 am | Reply

  8. I have MD simulation dcd files of 2 proteins interacting, and wanted to get the saltbridge distances between those 2 chains. I did it. But unfortunately one of the complex moves to top because of periodic boundary issue. And it gives wrong distance. Is there any solution for this problem? Since I has xst and xsc files with me, can I incorporate it with saltbridge tool? Or any other solution?

    Comment by Devanand T Santha — July 3, 2017 @ 1:35 pm | Reply


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