Re: [AMBER] docking evaluation using amber

From: George Tzotzos <>
Date: Mon, 14 Mar 2011 19:57:20 +0100


This is a good point but doesn't quite answer similar situations in blind docking.

Even in cases of cross-docking I have come across situations that the lowest energy conformation is not the same as the crystallographic model. Furthermore, increasing the number of evaluations does not improve matters. I'm my view, in such situations one cannot avoid a fully fledged MD simulation.

All the best


On Mar 14, 2011, at 2:32 PM, Dmitry Nilov wrote:

> Hello!
>> 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
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Received on Mon Mar 14 2011 - 12:00:03 PDT
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