Subject: Re: CCL:Rigid body dynamics

From: <[email-masked]>
Date: Mon, 17 Nov 1997 09:32:09 GMT

Richard Gillilan wrote:

> A number of programs (like XPLOR) have implemented the virtual
> rigid body dynamics of T. Head-Gordon and C. Brooks
> (Biopolymers vol 31, 77-100 (1991). I've seen a few notes
> on CCL about "Moldy" that sound like it too can do this.

I inspected Moldy's capabilities for rigid body protein docking (which I
right now do with XPLOR); it also implements the Newton-Euler equations of
motion which are used to propagate collections of rigid bodies. 
 
Moldy can be downloaded from earth.ox.ac.uk using anon ftp; relevant files
are in the /pub directory (information taken from Moldy 2.12). The author
is Keith Refson ([email-masked]).

> Also:
> 
> 1. Does anyone know of recent studies using this technique,
>    particularly applied to the protein-protein docking?

The recent protein-protein docking studies that I know of seem to choose
different ways of simplifying the proteins involved: Either a simplified
energy function (which takes into account only that part of the interaction
deemed relevant by the authors) is minimized using a MonteCarlo-Simulated
Annealing-like protocol, or the minimum is found by complete enumeration
(as in the case of the Fourier-convolution based approaches). All these
approaches trade a detailed description of the dynamics for docking speed. 
On the other side, some MD studies of docking have been performed (cf. Di
Nola et al., 1994). I haven't found any studies on protein-protein docking
using Head-Gordon's VRBD. 

As part of my current project, I'm studied protein-protein docking using
VRBD within XPLOR. Let me know if you're interested in my experiences.

> 2. How does it compare with SHAKE type constraint methods:
>    faster/slower or just different?

Just different would be a better description, as you constrain the bond
angles and dihedrals as well (dependent of course, on the way you choose
your rigid bodies). 
Second, in the SHAKE approach, each atom still experiences the force due to
it's interaction with the rest of the  system. In VRDB (as proposed by
Head-Gordon) , a force/torque acting on a  rigid body is derived from the
forces acting on it's constitutive atoms. 
Third, Head-Gordon in her work enforces planarity of the peptide bond by
turning it into a rigid body. Thus,  your dynamics will differ
>from a plain bond-length SHAKE simulation.

Hope this helps,

	Lutz Ehrlich

---------------------
Lutz Ehrlich

Structural Biology
EMBL
Meyerhofstr. 1
D-69012 Heidelberg
Germany

email: [email-masked]
web  : http://www.embl-heidelberg.de/~ehrlich
phone: +49-6221-387-140
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