Subject: Docking and binding affinity

From: "Ibrahim M.Moustafa" <[email-masked]>
Date: Wed, 28 Aug 2002 18:51:14 +0100

Dear CCL users,

   I have other questions concerning docking experiment.

    Is there any correlation between the binding constant, Ki, of the 
ligand and the ability of the docking program to predict its interaction 
with the binding site?

    Is there a lower limit for the binding constant below which predicting 
the ligand position becomes more difficult??

    Can we predict the binding of carbohydrate ligands which usually have 
binding affinity in the mM range?

    I wonder if people consider the binding constant when they select a set 
of ligands to validate their docking programs or they don't.

     Do they include ligands with low affinities in the testing set?

   Appreciated any comment  to clarify this point.

    Thanks for your help.

  Ibrahim

Ibrahim M.Mostafa
Center for Biomolecular Sciences,
Molecular Sciences Building,
North Haugh,St.Andrews,
Fife,KY16 9ST,
Scotland,U.K.
Tel.   +44-1334-467257
Fax   +44-1334-462595
e-mail: [email-masked]

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From: Yun Wang <[email-masked]>
Date: Thu, 29 Aug 2002 03:26:12 +0600 (GMT-6)

Hi, Dear CCLers,

  I plan to calculate the band structure of the surface. Could someone 
tell me how to choose the high-symmetry k-points, and where to find the 
coordinate for these k-points. Is there any website about this topic?
I have searched them by google, but there are little useful informations.
  Thanks for you reply. I shall summary it later.
  Best regards!

sincerely.
Yun Wang