This software uses rdc, chemical shift, and noe measurements. It also uses chemical shift and noe predictions. The program can use any number of media, e.g. peg, phage. The program uses a genetic algorithm to find the matching of measurements to residues. There is additional documentation in the Assign_SLP_1.12.

There are two related programs, MD2NOE_Protein and Assign_SLP_MD, which are not yet on glycam, which can also be found at the Prestegard Software site.

How to obtain the program

Click the green arrow in the graphic below to download the program files. Click on “DETAILS” to view additional information about the program.

ASSIGN SLP Redirect
ASSIGN_SLP_redirect.docx

11.8 KiB
443 Downloads
Details

This is a Matlab package that uses NMR experimental measurements and calculations in a genetic algorithm to sparsely label proteins. RDC's, noe's, and chemical shifts are used. The
software was developed in the Prestegard lab, and is available at that group's software website. I work in the Prestegard and Woods group at CCRC UGA and contribute software to glycam. Because we don't want multiple versions at different sites, only the link is given to the website. The package can be downloaded from

http://tesla.ccrc.uga.edu/software/ASSIGN_SLP/Assign_SLP_1.12.zip

Feel free to download from here and there. If you hit download here you won't get anything, except it will show how many downloads there are - so please hit the download here so we can keep track of how much usage there is, which is important.

Author:	Qi Gao, Gordon Chalmers, Kelly Moreman, James Prestegard
Category:	Publication Software
License:	CC Attribution-NonCommercial-ShareAlike
Documentation:	Documentation is included.
Associated Publications:	Submitted to the Journal of Biomolecular NMR. "NMR Assignments of Sparsely Labeled Proteins Using a Genetic Algorithm," Qi Gao^*; Gordon R Chalmers^*; Kelley W Moremen; James H Prestegard.
Date:	January 24, 2017

The download gives a file showing where to find the program.  It, and the documentation, can be found at the Prestegard software site, http://tesla.ccrc.uga.edu/software/.  We did not want multiple versions on 2 sites, and the work was primarily done with Professor Prestegard.

The program is also available for download here:

Software Downloads

Associated Publication

Pederson, K., Chalmers, G. R., Gao, Q., Elnatan, D., Ramelot, T. A., Ma, L. C., Montelione, G. T., Kennedy, M. A., Agard, D. A., and Prestegard, J. H. (2017) NMR characterization of HtpG, the E-coli Hsp90, using sparse labeling with C-13-methyl alanine, Journal of Biomolecular Nmr 68, 225-236.

Installation

Installation instructions are included in the download referenced at the top of this page.

Usage

Use instructions are included in the download referenced at the top of this page.

Click the green arrow in the graphic below to download the program files. Click on “DETAILS” to view additional information about the program.

This program uses Amber trajectories to calculate average 3J couplings.  It also produces histograms of 3-bond torsion angles from -180 to 180 degrees from the trajectories.  There are several types of options that the program can use.