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A tool to calculate Cremer-Pople parameters for rings in AMBER trajectories.
Languages: | English |
Author: | Spandana Makeneni |
Platforms: | Linux, Mac OS X |
Requirements: | GLYLIB |
Category: | Analysis Utilities |
License: | CC Attribution-NonCommercial-ShareAlike |
Related Publications: | JOURNAL OF THE AMERICAN CHEMICAL SOCIETY; Volume: 97 Issue: 6 Pages: 1354-1358 DOI: 10.1021/ja00839a011 Published: 1975 |
Other Contributors: | Lachele Foley |
Date: | April 8, 2014 |
Program for identifying the residue names of carbohydrates in a PDB file
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.
Author: | David F. Thieker |
Category: | Publication Software |
License: | CC Attribution-NonCommercial-ShareAlike |
Documentation: | Full documentation is available at http://glycam.org/3d-snfg |
Associated Publications: | Thieker, D. F., Hadden, J. A., Schulten, K. & Woods, R. J. (2016). "3D Implementation of the Symbol Nomenclature for Graphical Representation of Glycans." Glycobiology, (In Progress) |
Related Publications: | Varki, A., Cummings, R. D., Aebi, M., Packer, N. H., Seeberger, P. H., Esko, J. D., ... & Prestegard, J. J. (2015). "Symbol Nomenclature for Graphical Representations of Glycans." Glycobiology, 25 (12), 1323-1324. DOI: 10.1093/glycob/cwv091 |
Other Contributors: | Jodi A. Hadden, Klaus K. Schulten, & Robert J. Woods |
Date: | June 21, 2016 |
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.
Author: | David F. Thieker |
Category: | Publication Software |
License: | Apache 2.0 |
Documentation: | Full documentation is available at http://glycam.org/3d-snfg |
Associated Publications: | Thieker, D. F., Hadden, J. A., Schulten, K. & Woods, R. J. (2016). "3D Implementation of the Symbol Nomenclature for Graphical Representation of Glycans." Glycobiology, (In Progress) |
Related Publications: | Varki, A., Cummings, R. D., Aebi, M., Packer, N. H., Seeberger, P. H., Esko, J. D., ... & Prestegard, J. J. (2015). "Symbol Nomenclature for Graphical Representations of Glycans." Glycobiology, 25 (12), 1323-1324. DOI: 10.1093/glycob/cwv091 |
Other Contributors: | Jodi A. Hadden, Klaus K. Schulten, & Robert J. Woods |
Date: | July 11, 2016 |
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.
Author: | David F. Thieker |
Category: | Publication Software |
License: | CC Attribution-NonCommercial-ShareAlike |
Documentation: | Full documentation is available at http://glycam.org/3d-snfg |
Associated Publications: | Thieker, D. F., Hadden, J. A., Schulten, K. & Woods, R. J. (2016). "3D Implementation of the Symbol Nomenclature for Graphical Representation of Glycans." Glycobiology, (In Progress) |
Related Publications: | Varki, A., Cummings, R. D., Aebi, M., Packer, N. H., Seeberger, P. H., Esko, J. D., ... & Prestegard, J. J. (2015). "Symbol Nomenclature for Graphical Representations of Glycans." Glycobiology, 25 (12), 1323-1324. DOI: 10.1093/glycob/cwv091 |
Other Contributors: | Jodi A. Hadden, Klaus K. Schulten, & Robert J. Woods |
Date: | June 21, 2016 |
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.
Author: | David F. Thieker |
Category: | Publication Software |
License: | CC Attribution-NonCommercial-ShareAlike |
Documentation: | Full documentation is available at http://glycam.org/3d-snfg |
Associated Publications: | Thieker, D. F., Hadden, J. A., Schulten, K. & Woods, R. J. (2016). "3D Implementation of the Symbol Nomenclature for Graphical Representation of Glycans." Glycobiology, (In Progress) |
Related Publications: | Varki, A., Cummings, R. D., Aebi, M., Packer, N. H., Seeberger, P. H., Esko, J. D., ... & Prestegard, J. J. (2015). "Symbol Nomenclature for Graphical Representations of Glycans." Glycobiology, 25 (12), 1323-1324. DOI: 10.1093/glycob/cwv091 |
Other Contributors: | Jodi A. Hadden, Klaus K. Schulten, & Robert J. Woods |
Date: | June 21, 2016 |
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.
Author: | Lachele Foley |
Platforms: | Linux |
Requirements: | GLYLIB |
Category: | Publication Software |
License: | GLYLIB |
Documentation: | |
Other Contributors: | Spandana Makeneni |
Notes: | Unless you have reason to need this version, we recommend using a more updated GLYLIB. |
Date: | July 28, 2014 |
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 |
A tool for identifying ring conformations of pyranoses.
Author: | Spandana Makeneni |
Platforms: | Linux, Mac OS X |
Requirements: | GLYLIB |
Category: | Publication Software |
License: | CC Attribution-NonCommercial-ShareAlike |
Documentation: | Installation, running and other |
Associated Publications: | BFMP : A method for discretizing and visualizing pyranose conformations ; in review at the Journal of Chemical Information and Modeling |
Other Contributors: | Lachele Foley |
Date: | April 20, 2014 |
MD2NOE
MD2NOE.tar_.gz
Version: 1.1
This package enables users to calculate noes from Amber trajectories.
Languages: | English |
Author: | Gordon Chalmers |
Platforms: | Linux |
Requirements: | GLYLIB |
Category: | Publication Software |
License: | CC Attribution-NonCommercial-ShareAlike |
Documentation: | Documentation is included in the download. |
Associated Publications: | Chalmers G, Glushka JN, Foley BL, Woods RJ, Prestegard JH. Direct NOE simulation from long MD trajectories Journal of Magnetic Resonance. 265: 1-9. DOI: 10.1016/j.jmr.2016.01.006 |
Date: | January 19, 2017 |
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 |
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 |
Languages: | English |
Author: | Anita K. Nivedha, David F. Thieker |
Platforms: | Linux |
Category: | Publication Software |
License: | Apache 2.0 |
Associated Publications: | Vina-Carb: Improving Glycosidic Angles during Carbohydrate Docking |
Other Contributors: | Spandana Makeneni, Huimin Hu, Robert J. Woods |
Date: | August 31, 2015 |
Note that the libraries GLYLIB, GMML and GEMS are currently available only via their git repositories. For more information see SOFTWARE -> COMPUTING LIBRARIES, in the menu above.
Except for software listed under “Publication Software,” versions of software listed on this page are the most updated versions we recommend using. Those under “Publication Software” are the versions released with the publication; please see if an updated version is available. To see all versions of all files, browse the list of all downloadable files.