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 A
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
