Software Downloads

Click “DETAILS” in the icons below to view additional file information, including licensing and a link to the documentation.

Analysis Utilities

Cremer-Pople Trajectory Analysis Utility

Filename: cremer-pople.tgz

Size: 501.2 kB

Version: 2011-08-29

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Description:

A tool to calculate Cremer-Pople parameters for rings in AMBER trajectories.

Author:

Spandana Makeneni

Category:

Analysis Utilities

Platforms:

Linux, Mac OS X

Languages:

English

Requirements:

http://legacy.glycam.org/docs/othertoolsservice/software/computing-libraries/glylib/

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

Sugar identification program

Filename: sugarid_testing.tar.gz

Size: 115.1 kB

Version: No file version found

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Description:

Program for identifying the residue names of carbohydrates in a PDB file.

Author:

Spandana Makeneni, Lachele Foley

Category:

Analysis Utilities

Platforms:

Linux

Languages:

English

Requirements:

http://legacy.glycam.org/docs/othertoolsservice/software/computing-libraries/glylib/

Date:

Sept. 19, 2014

Publication Software

3D-SNFG Option 1 (Linux/Macintosh)

Filename: 3D-SNFG_v1_default-vmdrc_Linux-Mac.zip

Size: 15.7 kB

Version: 1

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Description:

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

Platforms:

Linux, Macintosh

Languages:

English

Documentation:

http://legacy.glycam.org/docs/othertoolsservice/2016/06/03/3d-symbol-nomenclature-for-glycans-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

3D-SNFG Option 1 (Windows)

Filename: 3D-SNFG_v1_default-vmdrc_Windows.zip

Size: 15.7kB

Version: 1

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Description:

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

Platforms:

Windows

Languages:

English

Documentation:

http://legacy.glycam.org/docs/othertoolsservice/2016/06/03/3d-symbol-nomenclature-for-glycans-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:

Other Contributors:

Jodi A. Hadden, Klaus K. Schulten, & Robert J. Woods

Date:

July 11, 2016

3D-SNFG Option 2 (Linux/Macintosh)

Filename: 3D-SNFG_v1_mod-vmdrc_Linux-Mac.zip

Size: 15.8 kB

Version: 1

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Description:

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

Platforms:

Linux/Macintosh

Languages:

English

Documentation:

http://legacy.glycam.org/docs/othertoolsservice/2016/06/03/3d-symbol-nomenclature-for-glycans-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:

Other Contributors:

Jodi A. Hadden, Klaus K. Schulten, & Robert J. Woods

Date:

June 21, 2016

3D-SNFG Option 2 (Windows)

Filename: 3D-SNFG_v1_mod-vmdrc_Windows.zip

Size: 15.8 kB

Version: 1

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Description:

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

Platforms:

Windows

Languages:

English

Documentation:

http://legacy.glycam.org/docs/othertoolsservice/2016/06/03/3d-symbol-nomenclature-for-glycans-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:

Other Contributors:

Jodi A. Hadden, Klaus K. Schulten, & Robert J. Woods

Date:

June 21, 2016

Archived GLYLIB for BFMP initial release

Filename: GLYLIB_BFMP_Archive.tar.gz

Size: 154.3 kB

Version: commit 159d12cb1983b28ad7affcde47149039729e60b7

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Description:

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

Author:

Lachele Foley

Category:

Publication Software

Platforms:

Linux

Languages:

English

Documentation:

http://legacy.glycam.org/docs/othertoolsservice/software/computing-libraries/glylib/

Date:

July 28, 2014

ASSIGN SLP Redirect

Filename: ASSIGN_SLP_redirect.docx

Size: 12 kB

Version: No file version found

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Description:

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.

Author:

Qi Gao, Gordon Chalmers, Kelly Moreman, James Prestegard

Category:

Publication Software

Languages:

English

Date:

Jan. 24, 2017

BFMP-shape identification program

Filename: BFMP.tar.gz

Size: 390.3 kB

Version: 1.0

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Description:

A tool for identifying ring conformations of pyranoses.

Author:

Spandana Makeneni

Category:

Publication Software

Platforms:

Linux, Mac OS X

Languages:

English

Date:

April 20, 2014

Vina-Carb with CH-Pi

Filename: VinaCarb_CHpi_20230608.zip

Size: 29MB

Version: 1.1.2

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Description:

The Vina-Carb software with a CH-Pi term added to scoring function, achieving improved performance level in CASF-2016 docking.

Author:

Yao Xiao and Robert J. Woods

Category:

Publication Software

Platforms:

Linux

Languages:

English

Documentation:

No documentation from us. Check the official Vina documentation at: https://vina.scripps.edu/manual/

Associated Publications:

(Under review): Xiao, Y.; Woods, R. J., Protein-ligand CH-Pi interactions: structural informatics, function development, and docking implementation. J. Chem. Theory Comput. 2023

Related Publications:

Trott, O., & Olson, A. J. (2010). AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of computational chemistry, 31(2), 455-461. Nivedha, A. K., "Thieker, D. F., Makeneni, S., Hu, H., & Woods, R. J. (2016). Vina-Carb: improving glycosidic angles during carbohydrate docking. Journal of chemical theory and computation, 12(2), 892-901.

Date:

June 8, 2023

Software Downloads

Click “DETAILS” in the icons below to view additional file information, including licensing and a link to the documentation.

Analysis Utilities

Cremer-Pople Trajectory Analysis Utility

Sugar identification program

Publication Software

3D-SNFG Option 1 (Linux/Macintosh)

3D-SNFG Option 1 (Windows)

3D-SNFG Option 2 (Linux/Macintosh)

3D-SNFG Option 2 (Windows)

Archived GLYLIB for BFMP initial release

ASSIGN SLP Redirect

BFMP-shape identification program

Vina-Carb with CH-Pi

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