Subject: water in ligand docking

From: Oliver Hucke <[email-masked]>
Date: Tue, 24 Jul 2001 11:20:40 +0200

Dear CCLers,

we are performing ligand docking calculations with the program FlexX.
Within the binding site there are ~20 water molecules visible in the
crystal structure.
Since FlexX considers the binding site as rigid, we have to decide which
of these water molecules to keep as part of the receptor.
(Unfortunately the 'particle mode' of FlexX did not produce satisfactory
results)

We are very interested in recommendations on how to select the water
molecules and/or in any experience/references concerning the subject of
considering water molecules in the binding site in ligand docking
calculations.

We will summarize the answers, of course.

Kind regards,

Tom Steinbrecher

______________________________________
Inst. fuer Physikalische Chemie II
Universitaet Freiburg
Albertstr. 23a
D-79104 Freiburg

Tel. :  +49-761-203-5130 (/-6179)
Fax. :  +49-761-203-6189
email:  [email-masked]
______________________________________