Re: [modeller_usage] Adding ligand in protein will solve sidechain confromatin problem?

[J B Procter <>]

A quick answer to you question about ligands, Nataraj.

This paper :
http://dx.doi.org/10.1016/j.jmb.2003.09.032
Evers, Gohlke, Klebe, Ligand-Supported Homology Modelling of Protein
Binding-sites using knowledge based potentials J.Mol.Bio. 334(2) 327-345

Describes the results of blending a ligand-protein docking function with
Modeller's objective function. This approach is a shortcut to getting a
good conformation for the complex without a full physical treatment of
the protein-ligand interaction. The full treatment is possible (can
someone correct me here!) if modeller has parameters for both your
ligand and its interactions with the protein. Sometimes you can do
this by explicitly specifying restraints (hydrogen bonds and salt
bridges). Either way, you should always get a better model of the
ligand-protein complex because you have used more information in the
modelling process.

So your answers :
> 1)Wheather my this idea is theoreticaly correct ?
Yes.

> 2)if the answer for my question 1 is correct, what is the way or
> routine which I can use it for adding my ligand(small
> molecule,eg.,DDT) to my model?
Look at the FAQ's about parameterising, adding ligands, and setting
explicit restraints for things like hydrogen bonding, coordination
geometry (metal centers). I know of no single function that
will do all this automatically (yet).

hope this helps.
j.