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