Yeyyyy!! The preprint for Glycam-Web is out! ⬇️ Super congrats @olivercgrant.bsky.social and all! Glycam-Web is a 🔝 complex carbohydrate builder, very accurate and intuitive while fast. We use it *ALL the time*, so I am delighted that now I can cite it properly 👍🤩 doi.org/10.1101/2025...
Generating 3D Models of Carbohydrates with GLYCAM-Web
The carbohydrate 3D structure-prediction tools (builders) at GLYCAM-Web ([glycam.org][1]) are widely used for generating experimentally-consistent 3D structures of oligosaccharides suitable for data i...
doi.org
May 22, 2025 at 8:53 AM
Yeyyyy!! The preprint for Glycam-Web is out! ⬇️ Super congrats @olivercgrant.bsky.social and all! Glycam-Web is a 🔝 complex carbohydrate builder, very accurate and intuitive while fast. We use it *ALL the time*, so I am delighted that now I can cite it properly 👍🤩 doi.org/10.1101/2025...
GLYCAM-Web offers a suite of validated 3D oligosaccharide structure modeling tools via a convenient web server.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Generating 3D models of complex carbohydrates with GLYCAM-Web - Nature Methods
GLYCAM-Web offers a suite of validated 3D oligosaccharide structure modeling tools via a convenient web server.
www.nature.com
March 23, 2026 at 4:18 PM
GLYCAM-Web offers a suite of validated 3D oligosaccharide structure modeling tools via a convenient web server.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Bacterial glycans are a nightmare to model.
Unusual sugars, missing parameters…
I’ve been working on extending the GLYCAM builder to include them — together with @robertamarchetti.bsky.social, @olivercgrant.bsky.social and the group of Prof. Woods.
Preprint👇
www.biorxiv.org/content/10.6...
Unusual sugars, missing parameters…
I’ve been working on extending the GLYCAM builder to include them — together with @robertamarchetti.bsky.social, @olivercgrant.bsky.social and the group of Prof. Woods.
Preprint👇
www.biorxiv.org/content/10.6...
April 8, 2026 at 2:24 PM
Bacterial glycans are a nightmare to model.
Unusual sugars, missing parameters…
I’ve been working on extending the GLYCAM builder to include them — together with @robertamarchetti.bsky.social, @olivercgrant.bsky.social and the group of Prof. Woods.
Preprint👇
www.biorxiv.org/content/10.6...
Unusual sugars, missing parameters…
I’ve been working on extending the GLYCAM builder to include them — together with @robertamarchetti.bsky.social, @olivercgrant.bsky.social and the group of Prof. Woods.
Preprint👇
www.biorxiv.org/content/10.6...
After 20 years and a recent big overhaul we're finally publishing the carbohydrate 3D structure builders on GLYCAM-Web (glycam.org)! Pre-print: (www.biorxiv.org/content/10.1...) #glycotime tools
Generating 3D Models of Carbohydrates with GLYCAM-Web
The carbohydrate 3D structure-prediction tools (builders) at GLYCAM-Web (glycam.org) are widely used for generating experimentally-consistent 3D structures of oligosaccharides suitable for data interp...
www.biorxiv.org
May 9, 2025 at 12:47 PM
After 20 years and a recent big overhaul we're finally publishing the carbohydrate 3D structure builders on GLYCAM-Web (glycam.org)! Pre-print: (www.biorxiv.org/content/10.1...) #glycotime tools
GLYCAM Bacterial Carbohydrate Builder: a web-tool for modelling 3D structures of bacterial glycans https://www.biorxiv.org/content/10.64898/2026.01.26.700271v1
January 27, 2026 at 11:46 AM
GLYCAM Bacterial Carbohydrate Builder: a web-tool for modelling 3D structures of bacterial glycans https://www.biorxiv.org/content/10.64898/2026.01.26.700271v1
Have you tried using Glycam?
December 6, 2024 at 9:18 AM
Have you tried using Glycam?
Thanks for the hint. I haven't because we would really like to stick to the CHARMM36 FF and Glycam is only giving glycam06, so the Amber FF version.
December 6, 2024 at 11:52 AM
Thanks for the hint. I haven't because we would really like to stick to the CHARMM36 FF and Glycam is only giving glycam06, so the Amber FF version.
You can now use repeat units, so to build 25 repeats of the capsular polysaccharide from group B streptococcus (serotype III) you go to glycam.org/txt and enter
[4DGlcpb1-6[DNeup5Aca2-3DGalpb1-4]DGlcpNAcb1-3DGalpb1-]<25>OH.
[4DGlcpb1-6[DNeup5Aca2-3DGalpb1-4]DGlcpNAcb1-3DGalpb1-]<25>OH.
GLYCAM-Web | Utilities for molecular modeling of carbohydrates
Utilities for molecular modeling of carbohydrates.
glycam.org
May 9, 2025 at 12:51 PM
You can now use repeat units, so to build 25 repeats of the capsular polysaccharide from group B streptococcus (serotype III) you go to glycam.org/txt and enter
[4DGlcpb1-6[DNeup5Aca2-3DGalpb1-4]DGlcpNAcb1-3DGalpb1-]<25>OH.
[4DGlcpb1-6[DNeup5Aca2-3DGalpb1-4]DGlcpNAcb1-3DGalpb1-]<25>OH.
I knew it would be hard… glad Glycam came in clutch
December 22, 2024 at 6:02 PM
I knew it would be hard… glad Glycam came in clutch
Thanks for all the comments!
Here comes my "not so elegant but so far only" solution as a Christmas gift 🎄
1. Build correct structure with glycam.org
2. Reorder and rename atoms to fit CHARMM convention topology from Charmm-gui
3. Use topology & FF files from Charmm-gui with corrected structure
Here comes my "not so elegant but so far only" solution as a Christmas gift 🎄
1. Build correct structure with glycam.org
2. Reorder and rename atoms to fit CHARMM convention topology from Charmm-gui
3. Use topology & FF files from Charmm-gui with corrected structure
December 22, 2024 at 11:21 AM
Thanks for all the comments!
Here comes my "not so elegant but so far only" solution as a Christmas gift 🎄
1. Build correct structure with glycam.org
2. Reorder and rename atoms to fit CHARMM convention topology from Charmm-gui
3. Use topology & FF files from Charmm-gui with corrected structure
Here comes my "not so elegant but so far only" solution as a Christmas gift 🎄
1. Build correct structure with glycam.org
2. Reorder and rename atoms to fit CHARMM convention topology from Charmm-gui
3. Use topology & FF files from Charmm-gui with corrected structure
Super proud to share with all of you the huge work we did to build the #GLYCAM Bacterial Carbohydrate Builder! @fnieto-fabregat.bsky.social @RobertWoods @OliverGrant
Bacterial glycans are a nightmare to model.
Unusual sugars, missing parameters…
I’ve been working on extending the GLYCAM builder to include them — together with @robertamarchetti.bsky.social, @olivercgrant.bsky.social and the group of Prof. Woods.
Preprint👇
www.biorxiv.org/content/10.6...
Unusual sugars, missing parameters…
I’ve been working on extending the GLYCAM builder to include them — together with @robertamarchetti.bsky.social, @olivercgrant.bsky.social and the group of Prof. Woods.
Preprint👇
www.biorxiv.org/content/10.6...
April 8, 2026 at 3:01 PM
Super proud to share with all of you the huge work we did to build the #GLYCAM Bacterial Carbohydrate Builder! @fnieto-fabregat.bsky.social @RobertWoods @OliverGrant
I recently ran into horrors of mysterious atom names for Glycam force fields. There seemed to be no choice but to hand-follow bond connections from prep files, so I made this awk script to convert AMBER prep to Graphviz DOT for visualization. github.com/benfordslaw/...
Here's an N-Acetylglucosamine:
Here's an N-Acetylglucosamine:
February 20, 2025 at 4:47 AM
I recently ran into horrors of mysterious atom names for Glycam force fields. There seemed to be no choice but to hand-follow bond connections from prep files, so I made this awk script to convert AMBER prep to Graphviz DOT for visualization. github.com/benfordslaw/...
Here's an N-Acetylglucosamine:
Here's an N-Acetylglucosamine:
This ⬇️ is screenshot of the Advanced Settings I used to produce the ensemble shown in the picture above,
January 3, 2026 at 7:59 PM
This ⬇️ is screenshot of the Advanced Settings I used to produce the ensemble shown in the picture above,
Thanks @elisafadda.bsky.social for all the suggestions. I can build the correct structure with glycam.org (which is actually correct compared to charmm-gui) but yes, conversion to CHARMM FF will be a pain. Lets see :D
GLYCAM-Web | Utilities for molecular modeling of carbohydrates
Utilities for molecular modeling of carbohydrates.
glycam.org
December 6, 2024 at 12:02 PM
Thanks @elisafadda.bsky.social for all the suggestions. I can build the correct structure with glycam.org (which is actually correct compared to charmm-gui) but yes, conversion to CHARMM FF will be a pain. Lets see :D
Generating 3D models of complex carbohydrates with GLYCAM-Web | Nature Methods https://www.nature.com/articles/s41592-026-03033-w
Generating 3D models of complex carbohydrates with GLYCAM-Web - Nature Methods
GLYCAM-Web offers a suite of validated 3D oligosaccharide structure modeling tools via a convenient web server.
www.nature.com
March 23, 2026 at 10:40 PM
Generating 3D models of complex carbohydrates with GLYCAM-Web | Nature Methods https://www.nature.com/articles/s41592-026-03033-w
Or go directly via url: glycam.org/url/condensed/[4DGlcpb1-6[DNeup5Aca2-3DGalpb1-4]DGlcpNAcb1-3DGalpb1-]<25>OH
GLYCAM-Web | Utilities for molecular modeling of carbohydrates
Utilities for molecular modeling of carbohydrates.
https://glycam.org/url/condensed/[4DGlcpb1-6[DNeup5Aca2-3DGalpb1-4]DGlcpNAcb1-3DGalpb1-]<25>OH
May 9, 2025 at 12:51 PM
Or go directly via url: glycam.org/url/condensed/[4DGlcpb1-6[DNeup5Aca2-3DGalpb1-4]DGlcpNAcb1-3DGalpb1-]<25>OH
Generating 3D Models of Carbohydrates with GLYCAM-Web https://www.biorxiv.org/content/10.1101/2025.05.08.652828v1
May 9, 2025 at 10:49 AM
Generating 3D Models of Carbohydrates with GLYCAM-Web https://www.biorxiv.org/content/10.1101/2025.05.08.652828v1
GLYCAM Bacterial Carbohydrate Builder: a web-tool for modelling 3D structures of bacterial glycans https://www.biorxiv.org/content/10.64898/2026.01.26.700271v1
January 27, 2026 at 11:46 AM
GLYCAM Bacterial Carbohydrate Builder: a web-tool for modelling 3D structures of bacterial glycans https://www.biorxiv.org/content/10.64898/2026.01.26.700271v1
Generating 3D Models of Carbohydrates with GLYCAM-Web https://www.biorxiv.org/content/10.1101/2025.05.08.652828v1
May 9, 2025 at 10:49 AM
Generating 3D Models of Carbohydrates with GLYCAM-Web https://www.biorxiv.org/content/10.1101/2025.05.08.652828v1
They evaluate performance across major nomenclatures—including WURCS, GlycoCT, GLYCAM, LinearCode, CSDB-linear, Oxford, and GlycoWorkbench—achieving 98–100% coverage on more than 150,000 sequences with sub-millisecond processing times.
December 29, 2025 at 10:01 AM
They evaluate performance across major nomenclatures—including WURCS, GlycoCT, GLYCAM, LinearCode, CSDB-linear, Oxford, and GlycoWorkbench—achieving 98–100% coverage on more than 150,000 sequences with sub-millisecond processing times.