From owner-chemistry@ccl.net Tue Feb  1 10:38:00 2011
From: "Roman Efremov efremov-x-nmr.ru" <owner-chemistry###server.ccl.net>
To: CCL
Subject: CCL: Calculating surface hydrophobicity
Message-Id: <-43819-110201100532-30223-Y4a5wis1/cLLjRN4lFZgNg###server.ccl.net>
X-Original-From: Roman Efremov <efremov_._nmr.ru>
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Date: Tue, 01 Feb 2011 18:04:34 +0300
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Sent to CCL by: Roman Efremov [efremov]=[nmr.ru]
Hi Sumitro,

You can use our program PLATINUM (http://model.nmr.ru/platinum) for 
calculation, mapping and visualization of hydrophobic/hydrophilic 
properties of molecules (including proteins).
This software is based on the concept of molecular hydrophobicity 
potential (MHP) and provides an atomic-scale presentation of hydrophobic 
properties of molecules (e.g., on their surfaces).

Best regards,

Roman
---------------------------------------------------------------------------
Roman G. Efremov, Professor
Head of Laboratory of Biomolecular Modeling,
M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry,
Russian Academy of Sciences
Phone: (7-095) 336 20 00; E-mail: efremov{}nmr.ru
Web: model.nmr.ru
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31.01.2011 6:28, Sumitro Harjanto sharjanto[*]i2r.a-star.edu.sg пишет:
> Sent to CCL by: "Sumitro  Harjanto" [sharjanto::i2r.a-star.edu.sg]
> Hi ,
>
> I want to calculate the surface hydrophobicity of a protein molecule, but so
> far I only manage to use atomic partial charges as the estimate of the surface
> hydrophobicity, anyone can provide me some insight on how well is that as an
> estimate..?
>
> Also, it will be great help if anyone knows of any software/webtools/ that
> calculates surface hyrdrophobicity of protein, which generates some kind of
> grid output file. Thanks!
>
> (btw, my input file is in .pdb format)
>
> Cheers,
> Sumitro>
>