RE: Beginner's question on docking



 You should read "Automated docking using a Lamarckian Genetic
 Algorithm,....." by Morris, Goodsell, Olson, et. al.
 J. Comp. Chem. 19, 1639-1662, (1998)  It will answer several of your
 questions.
 -----Original Message-----
 From: Computational Chemistry List [mailto:chemistry-request
 %a% ccl.net]On
 Behalf Of Its August
 Sent: Wednesday, May 11, 2005 3:52 AM
 To: chemistry %a% ccl.net
 Subject: CCL:Beginner's question on docking
 Hello,
 I've two question on ligand docking. Excuse me for
 asking such very basic questions:
 1. Docking methods calculate Binding Free Energy
 differences( or Delta G) as a measure of binding
 Affinity.(Please correct me if I'm wrong). Is there
 any other Thermodynamic function that can replace
 Delta G as a measure of binding affinity for ?
 2. On Docking in a Grid: Docking programs like
 AUTODOCK evalutae the Energy of a molecule on a GRID.
 I beleive the a GRID point is nothing but a point in a
 3d Space for which u know the binding affinity of a
 particular chemical group precomputed at that GRID
 point.
 However in some pose of the ligands one particular
 chemical group MAY NOT EXACTLY fall in one of such
 GRID point(Whatever fine resolution the grid may have
 ) How to calcualte energy in that case? I've came
 across a term like GRID INTERPOLATION. Is that
 anything  to do with in such a case?
 Moreover I would like to know how additive are these
 interactions. That means the energy computed for an
 isolated chemical group in a GRID , is it equal for
 the same group in a ligand or in a set of different
 ligands? Do the other neighbouring chemical groups
 exert some effect? Are there any literature references
 for this?
 Thanks in advance
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