The 3D-SNFG script interfaces with the Visual Molecular Dynamics (VMD) program in order to apply the Symbol Nomenclature for Glycans (SNFG) to 3D coordinates of carbohydrate structures.

The 3D-SNFG script interfaces with the Visual Molecular Dynamics (VMD) program in order to apply the Symbol Nomenclature for Glycans (SNFG) to 3D coordinates of carbohydrate structures.

The 3D-SNFG script interfaces with the Visual Molecular Dynamics (VMD) program in order to apply the Symbol Nomenclature for Glycans (SNFG) to 3D coordinates of carbohydrate structures.

The 3D-SNFG script interfaces with the Visual Molecular Dynamics (VMD) program in order to apply the Symbol Nomenclature for Glycans (SNFG) to 3D coordinates of carbohydrate structures.

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.

This is a version of GLYLIB that was archived for historical purposes associated with the initial release of the BFMP program.

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.

A tool for identifying ring conformations of pyranoses.

This package enables users to calculate noes from Amber trajectories.

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.

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.

Input/Output files used in the BFMP tutorial 1.

Input/Output files used in BFMP tutorial 2

Simulation and setup files directly relevant to the paper referenced below.

Coordinate output file from the MD simulation of A-D-Idopyranose.

The prepfiles which were used to build the IdoA for the simulation in the BFMP paper