Re: [modeller_usage] Modeling ligands in the binding site

[Modeller Caretaker <modeller-care@ucsf.edu>]

On 11/22/2009 05:35 PM, Qinghua Liao wrote:
> Can modeller do ligand-steered modelling? And what is the difference
> between the ligand-steered method and the mothods from the on-line
> tutorial of Modeling ligands in the binding site? Are they the same
> method? Thanks very much!

Ligands can be handled in Modeller in two ways: either as flexible 
residues (if topology and parameters are present in the CHARMM 
forcefield files, modlib/top_heav.lib and modlib/par.lib) or as 'block' 
residues, where they are simply copied from template to target as rigid 
bodies. The examples in the tutorial use the latter method. Neither of 
these qualify as "ligand-steered" if by that you mean refinement of 
shape of the binding pocket - binding residues will be treated much like 
any other protein residue, and so will tend to look like the binding 
pocket in the template.

	Ben Webb, Modeller Caretaker
--
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