From chemistry-request "-at-" server.ccl.net Wed Feb 20 09:04:03 2002
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Date: Wed, 20 Feb 2002 09:03:41 -0500
From: Richard Gillilan <reg8*- at -*cornell.edu>
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Subject: Re: CCL:starting structure for docking
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"nepenthes -8 at 8- vplaces.net" wrote:
> 
> Dear CCLers,
> 
> I hope you will bear with this question of mine but I wasn't able to agree with my colleague about it. I've docking a molecule, citrulline, to a protein and I obtained the citrulline molecule from a protein-citrulline complex from the PDB database website. I think it's suitable by just extracting the citrulline sequence and adding hydrogen to it and minimized the structure later on before I start my docking process.

Sounds like you are treating the citrulline as a rigid body. Looks like there
are at least 5 rotatable bonds in that structure. You should really use 
flexible docking like Autodock. In that case the initial structure does not
matter, the torsion angles will be randomized during the Monte Carlo steps
and there should be no bias ... you are effectively performing minimization
of the ligand during the docking process. Bond length and angle changes are 
probably very minor.

Richard Gillilan
MacCHESS