Hi Heidi
You can try hunting for similar structural motifs which are likely
to be involved in ligand binding or function:
http://www.russelllab.org/cgi-bin/tools/pints.pl
You can then try fitting suggested ligands to the cavity.
good luck
Alex
On 10.08.2011 13:46, Heidi Tuominen wrote:
Dear All,
I have inside cavity in my protein structure with some conserved
residues. We do not know function or ligand for that domain.
How I could find ligand candidates which fit to this cavity? Maybe
somehow with pdbe?
Thank you,
Heidi
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Alexander V. Shkumatov, Ph.D.
Biological Small Angle Scattering Group
EMBL Hamburg Outstation c/o DESY tel: +49 40 89902 178
Building 25A Notkestraße 85 fax: +49 40 89902 149
22603 Hamburg, Germany email: ashku...@embl-hamburg.de
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