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Re: [modeller_usage] Modeling ligands in the binding site

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
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage