CCL: Calculating surface hydrophobicity

[Roman Efremov <efremov_._nmr.ru>]

 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
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 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
 ---------------------------------------------------------------------------
 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>