Subject: protein domain movements: a new algorithm

From: Willy Wriggers <[email-masked]>
Date: Mon, 18 Sep 95 17:03:33 -0500

Dear all,

I would like to present "Hingefind", a new algorithm to
determine and visualize protein domain movements by
comparing two structures. Below follows a short
description of the method. It has been developed to
investigate differences in crystal structures or
computer simulated systems and I found it very useful for
obtaining a coarse-grained description of the movements.

Please access the Hingefind homepage for more info and an
example of usage:
ftp://lisboa.ks.uiuc.edu/pub/wriggers/hingefind/hingefind.html

or download the whole distribution including
documentation by anonymous ftp to lisboa.ks.uiuc.edu
from the directory pub/wriggers/hingefind !

Cheers,
Willy Wriggers
_______________________________________________
[email-masked]		 (NeXT-mail OK)

Willy R. Wriggers
Theoretical Biophysics Group
Beckman Institute
University of Illinois at Urbana-Champaign
405 North Mathews Avenue
Urbana, IL 61801, USA

Telephone (217) 244-1612
Telefax (217) 244-6078
WorldWideWeb: http://www.ks.uiuc.edu/~wriggers/
_______________________________________________

"Hingefind" is an algorithm for the identification of
domain movements and their characterization and
visualization by hinge points and rotation axes. The
method is implemented in X-PLOR 3.1 script language
(Axel T. Brunger, 1992). The output psf and pdb files can
be visualized with standard graphics packages.  It
compares two known structures (e.g. two different
crystal structures of a protein or the results of
molecular dynamics simulations) and partitions the
protein with a prespecified resolution in preserved
subdomains. It then determines effective hingeaxes
which characterize the domain movements with respect to
the reference domain. Both parts of the algorithm can be
used alone, i.e. one can assign domains manually and let
the algorithm determine the effective hingeregions
between the domains, or one can use the algorithm to
partition a protein into preserved subdomains. The
method does not require any previous knowledge about
functionally relevant domains or hinge motions,
however a critical analysis of the results is
recommended. The output files provide information
about the accuracy of the found hinge-rotation. The
variety of options and resolutions allow to find an
optimal partitioning. The user can assess the validity
of the proposed movement and test a variety of
resolutions.