Hingefind

"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 one to find an optimal partitioning. The user can assess the validity of the proposed movement and test a variety of resolutions.

Please access the Hingefind homepage for more info and an example of usage: ftp://lisboa.ks.uiuc.edu/pub/hingefind/hingefind.html or download the whole distribution including documentation by anonymous ftp to lisboa.ks.uiuc.edu from the directory pub/hingefind

Contact: Willy R. Wriggers,
Theoretical Biophysics Group,
Beckman Institute,
University of Illinois at Urbana-Champaign,
405 North Mathews Avenue,
Urbana, IL 61801, USA,
Telephone: +1-217-244-1612,
Fax: +1-217-244-6078,
WWW: http://www.ks.uiuc.edu/~wriggers/
E-mail: wriggers@uiuc.edu

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