Re: [AMBER] docking evaluation using amber

From: Dmitry Nilov <>
Date: Mon, 14 Mar 2011 16:32:02 +0300


> We have docked a ligand to a protein using AUTODOCK 4.2.
> AUTODOCK  gives many docks that are structurally very different but "energetically" the similar.

I believe that the scoring function of docking program can estimate
accurately the energy of only correct (i.e. active for inhibitors and
reactive for substrates) ligand positions since it is just trained on
a set of protein-inhibitor crystallographic complexes.
Thus it is very good idea to use a reference position of ligand (e.g.
taken from crystallographic enzyme-competitive inhibitor complex) as
criterion of correctness of modeled position.

But even if modeled position is correct it can be strained in Amber
force field since it was obtained using soft van-der-vaals potential
of scoring function. Thus in some cases it is reasonable to restrain
ligand - (active site residues) distances during MD equilibration to
prevent instantaneous dissotiation.

Dmitry Nilov,
Faculty of Bioengineering and Bioinformatics,
Lomonosov Moscow State University
AMBER mailing list
Received on Mon Mar 14 2011 - 07:00:06 PDT
Custom Search