[gmx-users] RE: Docking Energy confirmation

Anton Feenstra feenstra at chem.vu.nl
Fri Dec 5 08:48:01 CET 2003

Spiwok Vojtech wrote:

>>I'm doing docking "calculations" with Autodock3.05.
>>My question is, is there any way to use the energy minimization procedure from
>>Gromacs to relax the conformations obtained from autodock and have a better estimate
>>of their energy (in comparision tothe energy that autodock gives as result)?
> If you prefer accuracy over throughput then Prodrug/gromacs minimization
> and dynamics could be a choice. Autodock uses its scoring function
> which includes force-field terms and empiricaly derived terms for solvent
> effect and conformational entropy of ligand. Therefore only force-field
> energy itself (either from gromacs or autodock) can hardly be a better
> for scoring of ligands. You might try free energy calculation by linear
> interaction energy (g_lie of gromacs).

In my experience, the LIE method (rougly implemented in g_lie), gives the
better estimate than the scoring function values from a docking program
like Autodock, IMHO mainly because entropic factors are taken into accoount
at least to some extent in LIE.

What I've also done is use docked conformations as starting points for MD,
and then cluster the resulting trajectories. It all depends very much
on the type of system you are looking at, e.g. the behaviour of the ligand,
the type of binding, the amount of internal degrees of freedom in the ligand,
the flexibility of the protein (and I'm sure anyone could think of a few
more caveats!).

Best way, IMHO, is to try it for your particular system and if possible
compare with experiment to determine the best performing method for you.


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |

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