Subject: AutoDock and protein-protein interactions

From: Dominique Vlieghe <Dominique.Vlieghe$at$dmbr.UGent.be>
Date: 04 Jul 2003 10:15:39 +0200

Hello all,

* A general question:
I was wondering whether AutoDock is suitable for studying
protein-protein interactions. In principle it is, but speed is the
practical limitation I presume. Does anyone have experience with this?

* a more specific question:
A way of circumventing a huge grid would be to use a smaller grid
(assuming that the interacting residues must be 'close' to the receptor)
and setting the extnrg parameters to 0.0 kcal mol-1 (meaning that atoms
outside the grid would feel no field). Is this a correct assumption?
Would this speed up the calculations?

Furthermore, are there other ways of avoiding the calculation of
interactions involving ligand atoms that are too far away from the
receptor? This would make sense, because in P-P interaction only a
'small' number of residues normally contribute to the interaction. Are
they any ways of doing this in AutoDock? 

Regards,

Dominique

P.S. What happened to the autodock mailing list?

-- 
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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)9-33-13.692
(new) Fax : +32-(0)9-33-13.609
(new) email:dominique.vlieghe$at$dmbr.ugent.be
(new) www:http://www.dmbr.ugent.be/
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