[Chimera-users] hydrophobic pocket

[Miguel Ortiz-Lombardía]

That's a good question...
In a first approximation you could assume that all atoms not classified as
acceptors/donors of protons would be hydrophobic. This is essentially
carbons. If you represent the surface of the molecule colored by elements
you should see these pockets.

More sophisticated approaches include the program GRID (
http://www.moldiscovery.com/soft_grid.php) to compute the hydrophobic
potential (Goodford, P.J., A computational procedure for determining
energetically favourable binding sites on biologically important
macromolecules. *J. Med. Chem. **28*, 849-57.)

Unfortunately, GRID is not free, not even for academics (though there is a
special price for the license). Anyway, I think it would be nice if chimera
could map the hydrophobic potential maps onto molecular surfaces.

Best,


Miguel

2008/6/27 bala <bala at igib.res.in>:

> Dear Chimerian's,
>
> How do i detect hydrophobic pockets in a protein using chimera ?.
>
> Thanks in advance,
> Bala
>
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