diff --git a/docs/community_tools.md b/docs/community_tools.md index 54c0cd76..e9dd2893 100644 --- a/docs/community_tools.md +++ b/docs/community_tools.md @@ -1,15 +1,33 @@ # Community Tools -## JAAG – JSON input file Assembler for AlphaFold 3 (with Glycan Integration) +## JAAG: a JSON input file Assembler for AlphaFold 3 (with Glycan Integration) -JAAG is a lightweight, web-based GUI tool that helps generate AlphaFold 3 input -JSON files with integrated glycan support. It automates the creation of correct -glycan syntax (including `bondedAtomPairs` + CCD), reducing manual errors when -preparing glycoprotein or glycan–protein systems. +JAAG is a lightweight, web-based GUI tool that helps generate AlphaFold 3 input JSON files with integrated glycan support. It automates the creation of correct glycan syntax (including `bondedAtomPairs` + CCD), reducing manual errors when preparing glycoprotein or glycan–protein complexes. * Web app: https://biofgreat.org/JAAG * Source code: https://github.com/chinchc/JAAG -* Preprint: https://www.biorxiv.org/content/10.1101/2025.10.08.681238v1 +* Reference: Chin Huang, Kelley W Moremen, Editor’s Choice JAAG: a JSON input file assembler for AlphaFold 3 with glycan integration, Glycobiology, Volume 36, Issue 1, January 2026, cwaf083, https://doi.org/10.1093/glycob/cwaf083 Note: JAAG is compatible with standalone AlphaFold 3, but not with the AlphaFold 3 server. + +## Modeling glycans with AlphaFold 3: capabilities, caveats, and limitations + +We would like to share our recent work on modeling glycans (and other ligands) with AF3. We modeled and assessed major glycan classes and provided practical resources: +* Step-by-step tutorial for building ligand inputs (applicable beyond glycans) +* Ready-to-run scripts for each glycan class +* Comprehensive CCD table for all SNFG monosaccharides +* Discussion of caveats and limitations of AF3 +* Full AF3 inputs/outputs openly archived on ModelArchive for reproducibility + +If your AF3 ligand models appear stereochemically off, give it another try! + +Reference: Chin Huang, Natarajan Kannan, Kelley W Moremen, Modeling glycans with AlphaFold 3: capabilities, caveats, and limitations, Glycobiology, Volume 35, Issue 10, October 2025, cwaf048, https://doi.org/10.1093/glycob/cwaf048 +ModelArchive: https://doi.org/10.5452/ma-af3glycan + +Thanks, +Chin Huang | Moremen Lab +Ph.D. Candidate & Graduate Research Assistant +Department of Biochemistry and Molecular Biology +Complex Carbohydrate Research Center +University of Georgia