Hydrophobic interactions

From: Luthra,Amit
Date: 14 December 2011 20:34

Hi Everyone

I have to calculate hydrophobic interactions in pdb files. Is any server available for this type of calculation?

 

Thanks in advance

 

Amit

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From: <eugene.krissinel


google on "pisa pdbe"  -- Eugene

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From: Vandana Kukshal


Dear amit sir ,,,,,,,,

                            you can go through this server ..........http://pic.mbu.iisc.ernet.in . PIC server can calculate many interactions within and between the protein molecules. ..""PIC: Protein Interactions Calculator K. G. Tina, R. Bhadra, and N. Srinivasan,NAR 2007""

best regards 

--
Vandana kukshal

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From: Iain Kerr

LIGPLOT will show this graphically, if the correct parameters are set in ligplot.prm, but not state the interactions explicitly:

http://www.ebi.ac.uk/thornton-srv/software/LIGPLOT/

The relevant lines in ligplot.prm:

PLOT PARAMETERS --------------- Y     <- Include: Hydrophobic interactions - (Y/N)?

HTH,
Iain