Subject: Re: CCL:Atomic contact energies

From: Dominique Vlieghe <Dominique.Vlieghe*at*dmbr.UGent.be>
Date: 08 Oct 2003 08:45:36 +0200

Hi Craig, hi rest,

On Tue, 2003-10-07 at 04:04, Craig Shepherd wrote:
> Hello all,
> 
> Does anyone know of a program (standalone or incorporated into some
> package) that will calculate atomic contact energies (ACE) for a protein 
> structure(s)?
> It seems that a lot of docking groups use them in their scoring 
> functions, so my
> hunch is the programs are out there.
> 

I asked Rong Chen - the author of ZDOCK and RDOCK - practically the same
question some time ago (but related to protein-protein docking), and
this is an excerpt of his reply:

... To calculate ACE energy, you just divide all protein atoms into 18
atom types, count the number of i-j atom pairs within 6 angstrom. Each
i-j atom pair gets an ACE score of deltaG(ij). Sum over all i-j pairs,
you will get the ACE energy for the protein complex. There is a program
called mark_sur.f in ZDOCK package to mark ACE types for all protein
atoms according to uniCHARMM, which is a parameter file included in
ZDOCK release. After marking ACE types for all atoms using mark_sur.f,
you can easily write a script to count the number of i-j atom pairs, and
sum over i and j to get the ACE energy for the whole complex...

Of course, what he is saying is basically: DIY :-)  So if someone knows
of such a ACE calculating tool, I'm also very interested

Regards,

Dominique

> So you know what I'm talking about, the ACE's I'm talking about are 
> described in
> the following references:
> 
> Miyazawa, S. and Jernigan, R.L. Estimation of effective interresidue 
> contact energies from
> protein crystal structures: quasi-chemical approximation.  1985.  
> /Macromolecules/ 18:534-552.
> 
> Zhang, C. /et al. /Determinations of atomic desolvation energies from 
> the structures of crystallized
> proteins. 1997.  /J. Mol. Biol. /267:707-726.
> 
> Thanks a lot,
> 
> Craig Shepherd
> 
> 
> 
> 
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-- 
------------------------------
Dominique Vlieghe, Ph.D.,
Bioinformatics Core,
Department for Molecular Biomedical Research (DMBR)
VIB - Ghent University
(new) 'Fiers-Schell-Van Montagu' building
(new) Technologiepark 927
(new) B-9052 Ghent (Zwijnaarde), Belgium

(new) Tel : +32-(0)9-33-13.693
(new) Fax : +32-(0)9-33-13.609
(new) email:dominique.vlieghe*at*dmbr.ugent.be
(new) www:http://www.dmbr.ugent.be/
------------------------------

---

From: Andreas Klamt <klamt:at:cosmologic.de>
Date: Wed, 08 Oct 2003 17:09:13 +0200

Just a thought regarding ACEs:
My COSMO-RS solvation model describes the free energy of molecules in 
the liquid phase by pairwise interactions of surfaces. But it makes use 
of surface polarization charge densities (sigma) of both surface 
segments, which result DFT/COSMO calculations. In case one should not be 
able to afford such calculations for the purpose you have in mind, you 
get approximate polarization charge densities from similar regions of 
molecules. We have a tool COSMOfrag to do so. Thus in the end you would 
be able to get an estimate of the entire interaction energies (and can 
simply subtract the desolvation free energy within the COSMO-RS theory). 
Even with the approximate sigma's this scheme should be more robust than 
just atom contact energies.

Please see our homepage for more information and references on COSMO-RS, 
and contact me for a eventual collaboration on the development of such 
scoring tool.

Regards

Andreas

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