Subject: useful software for dual domain protein conformational search?

From: olivier walker <[email-masked]>
Date: Fri, 27 Sep 2002 09:25:23 -0700

Hi all,

I'm currently studying a dual domain protein. I would like to generate all 
possible conformations including some restraints.
Basically, I want to study all possible conformation of the link between 
the two domains (8 residues) and freeze the two domains (not totally 
because I would like to follow the shift of the domains with the 
conformation change of the link).

My questions are:

* what method should I consider (MD, monte carlo, annealing.....)?
* The most important: what is the best suitable software for this kind of 
study ?
* using this software, is it possible to monitor energy, distances between 
given residues and other features?

Thanks in advance for your help

olivier.

**************************************************
Olivier WALKER
Department of Chemistry & Biochemistry
University of Maryland
College Park, MD 20742
USA
**************************************************
Fax : 301-314-0386
Phone : 301-405-8710
E-mail : [email-masked]
**************************************************

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From: David van der Spoel <[email-masked]>
Date: 27 Sep 2002 16:02:16 +0200

> * The most important: what is the best suitable software for this kind of 
you want to use dyndom first to define the hinge and rotation vectors:
http://asgard.sys.uea.ac.uk:8080/dyndom/main.jsp

> given residues and other features?
Then you can use GROMACS (http://www.gromacs.org, program g_dyndom) to
analyze the results, make interpolations and extrpolations of the
rotatiom motion

-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
[email-masked]	[email-masked]   http://zorn.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

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From: Richard Gillilan <[email-masked]>
Date: Fri, 27 Sep 2002 10:50:05 -0400

This sounds like a good candidate for rigid-body
mechanics. You could treat the two domains as rigid
but NOT fixed in space. You could also apply additional
constraints to the bond lengths if you wanted to increase the
efficiency of the dynamics run. I believe the MBO(N)D program
available from (Accelrys?) can do this sort of thing.
There were a couple papers in J. Comp. Chem. on combining 
quaternion-based mechanics with SHAKE-type constraints
a few years ago:

    Forester TR, Smith W
    SHAKE, rattle, and roll: Efficient constraint algorithms for linked rigid bodies
    J COMPUT CHEM 19 (1): 102-111 JAN 15 1998)

    Wu XW, Sung SS
    Constraint dynamics algorithm for simulation of semiflexible macromolecules
    J COMPUT CHEM 19 (14): 1555-1566 NOV 15 1998 

Richard Gillilan
MacCHESS, Cornell