This program uses a pdb and topology file to calculate 3J couplings and NOE’s.  This calculation is approximate because only a single frame is used and with the 1/r^6 approximation for the NOE calculation.  There are additional improvements to be added soon such as the inclusion of STD NOE’s and output of 2d NOESY spectra (simulated).  These improvements are done, but not yet included.

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.

SingleFrameNMR
SingleFrameNMR.tar_.gz
Version: 1.0

941.4 KiB
258 Downloads
Details

This software uses a pdb and topology file to calculate noe's and 3J couplings. Documentation is included. The calculation is approximate due to the use only of a single frame and not a trajectory. It will eventually be used to provide the user these nmr observables in the download of a structure at glycam. The package can be downloaded now.

Languages:	English
Author:	Gordon Chalmers
Platforms:	Linux
Requirements:	GLYLIB
Category:	Publication Software
License:	CC Attribution-NonCommercial-ShareAlike
Documentation:	Documentation is included.
Other Contributors:	Rob Woods
Date:	June 22, 2017

The program is also available for download here:

Software Downloads

Associated Publication

Direct NOE Simulation from Long MD Trajectories.  G. Chalmers, J.N. Glushka, B.L. Foley, R.J. Woods, J.H. Prestegard.  Journal of Magnetic Resonance.  2016.  http://dx.doi.org/10.1016/j.jmr.2016.01.006

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.

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.

How to obtain 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.

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.

3J_coupling_distribution
3J_coupling_distribution.tar_.gz
Version: 1.1

1.3 MiB
430 Downloads
Details

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. Program error corrected.

Languages:	English
Author:	Gordon Chalmers
Platforms:	Linux
Requirements:	GLYLIB
Category:	Publication Software
License:	CC Attribution-NonCommercial-ShareAlike
Documentation:	Documentation is included
Other Contributors:	Rob Woods, Lachele Foley
Date:	April 18, 2016

The program is also available for download here:

Software Downloads

Associated Publication

None

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.

This is a package that calculates spin-spin and spin-lattice relaxation rates from trajectories.  This program can be used for well-sampled trajectories such as small molecules, and also with large molecules such as proteins and in not so well sampled trajectories.  In the latter case the ‘sphere’ approximation is used in which an artificial tumbling is added to a frame aligned trajectory.  This sphere approximation substantially improves the sampling.  The software has been successfully used with work on the skp1 protein.

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.

particular_relaxation_rate
particular_relaxation_rate.tar_.gz
Version: 1.0

107.9 MiB
239 Downloads
Details

This is a package that calculations spin-spin and spin-lattice relaxation rates. The program can be used for well sampled trajectories, as found in small molecules, and also for proteins. In the latter case, the non-well sampled trajectory is handled by a 'sphere approximation,' in which artificial tumbling is added to the frame aligned trajectory. This substantially improves the sampling. As always, I am sure there will be some minor revisions.

Languages:	English
Author:	Gordon Chalmers
Platforms:	Linux
Requirements:	GLYLIB
Category:	Publication Software
License:	CC Attribution-NonCommercial-ShareAlike
Documentation:	Documentation and examples are included.
Associated Publications:	Glycosylation modulates the F-box combining site in Dictyostelium Skp1, M. Osman Sheikh, David Thieker, Christopher M. Schafer, Gordon Chalmers, Xianzhong Xu, Robert Woods, John N. Glushka, Brad Bendiak, James H. Prestegard, and Christopher M. West, to be submitted.
Date:	April 18, 2017

The program is also available for download here:

Software Downloads

Associated Publication

Glycosylation associated with O2-sensing modulates the F-box combining site of Dictyostelium Skp1, JBC,

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.

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
444 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.