pepflex - v2.0 (1995)

Purpose: - evaluates structures of flexible proteins


Description

This program calculates NOE intensities for user-defined and produced structures of a peptide. The calculated NOE's are compared to experimental data and the deviation is quantified in form of an R-Factor (as in xray crystallography) or an RMSD (root mean square deviation).

The user is prompted to enter several input parameters. It is most convenient to place these parameters in a file (eg, test.run) and then run the program as follows:

    pepflex < test.run 


Parameters


	output     results file for this run
	0          echo input data (0=no, 1=yes)
	500.0      spectrometer frequency
	1.00       correlation time (tauc) in ns
	0.0        external relaxation rate (1/sec)
	xxx.arc    biosym archive file
	1          structure to use in calculation
	3-6        structure to use in calculation
	0          indicates end of structure list
	xxx.asn    asn (atom labels) file (MAX 1000 Noes)
	xxx.pks    noe intensities file (.pks format)
	300.0      mixing time for noe data (in ms)
	1          crosspeak table output (1=sorted, 2=NOT)
	20.0       threshold for reporting NOEs not in asn file


Notes


Installation and Download

Executable versions of this program for suns or sgis are freely available at our ftp site. First you will need to download the software from our website:

Once you have downloaded the software, you then proceed by uncompressing and untarring the files:
	uncompress downloadfile.tar.Z
	tar xvf downloadfile.tar

You should then take a look at the README file to understand what files are being installed and the installation options you have. After this, type "Install" to put the files in the appropriate places.


Authors

Authors: Jianjun Wang, Frank D Sonnichsen, Robert Boyko, Robert Hodges, Brian Sykes

Funding for this project has been provided by the Medical Research Council of Canada and the Protein Engineering Networks of Centres of Excellence (Canada).

Reference:

	Techniques in Protein Chemistry IV, 1993
	Evaluation of NMR Based Structure Determination of Flexible Peptides:
	Application to Desmopressin p.569


Last modified: May 14, 1997

Robert Boyko - robert.boyko@ualberta.ca