Software Downloads

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Analysis Utilities

Cremer-Pople Trajectory Analysis Utility

cremer-pople.tgz
501.2 kB
2011-08-29
A tool to calculate Cremer-Pople parameters for rings in AMBER trajectories.
Spandana Makeneni
Analysis Utilities
Linux, Mac OS X
English
Lachele Foley
April 8, 2014

Sugar identification program

sugarid_testing.tar.gz
115.1 kB
No file version found
Program for identifying the residue names of carbohydrates in a PDB file.
Spandana Makeneni, Lachele Foley
Analysis Utilities
Linux
English
Sept. 19, 2014

Publication Software

3D-SNFG Option 1 (Linux/Macintosh)

3D-SNFG_v1_default-vmdrc_Linux-Mac.zip
15.7 kB
1
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.
David F. Thieker
Publication Software
Linux, Macintosh
English
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)
Jodi A. Hadden, Klaus K. Schulten, & Robert J. Woods
June 21, 2016

3D-SNFG Option 1 (Windows)

3D-SNFG_v1_default-vmdrc_Windows.zip
15.7kB
1
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.
David F. Thieker
Publication Software
Windows
English
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)
Jodi A. Hadden, Klaus K. Schulten, & Robert J. Woods
July 11, 2016

3D-SNFG Option 2 (Linux/Macintosh)

3D-SNFG_v1_mod-vmdrc_Linux-Mac.zip
15.8 kB
1
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.
David F. Thieker
Publication Software
Linux/Macintosh
English
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)
Jodi A. Hadden, Klaus K. Schulten, & Robert J. Woods
June 21, 2016

3D-SNFG Option 2 (Windows)

3D-SNFG_v1_mod-vmdrc_Windows.zip
15.8 kB
1
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.
David F. Thieker
Publication Software
Windows
English
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)
Jodi A. Hadden, Klaus K. Schulten, & Robert J. Woods
June 21, 2016

Archived GLYLIB for BFMP initial release

GLYLIB_BFMP_Archive.tar.gz
154.3 kB
commit 159d12cb1983b28ad7affcde47149039729e60b7
This is a version of GLYLIB that was archived for historical purposes associated with the initial release of the BFMP program.
Lachele Foley
Publication Software
Linux
English
July 28, 2014

ASSIGN SLP Redirect

ASSIGN_SLP_redirect.docx
12 kB
No file version found
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.
Qi Gao, Gordon Chalmers, Kelly Moreman, James Prestegard
Publication Software
English
Jan. 24, 2017

BFMP-shape identification program

BFMP.tar.gz
390.3 kB
1.0
A tool for identifying ring conformations of pyranoses.
Spandana Makeneni
Publication Software
Linux, Mac OS X
English
April 20, 2014

Vina-Carb with CH-Pi

VinaCarb_CHpi_20230608.zip
29MB
1.1.2
The Vina-Carb software with a CH-Pi term added to scoring function, achieving improved performance level in CASF-2016 docking.
Yao Xiao and Robert J. Woods
Publication Software
Linux
English
(Under review): Xiao, Y.; Woods, R. J., Protein-ligand CH-Pi interactions: structural informatics, function development, and docking implementation. J. Chem. Theory Comput. 2023
June 8, 2023