Add the glycan modeling paper in the list of community tools

Adapted from https://github.com/google-deepmind/alphafold3/pull/608/changes, thanks @chinchc.

PiperOrigin-RevId: 862720014
Change-Id: I021eef0b46158e8ce28e97d9172ba6e79ef3f30c

docs/community_tools.md

@@ -1,15 +1,31 @@
 # 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.
+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
+*   Paper: 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
+
+Paper on modeling glycans (and other ligands) with AF3 that modeled and assessed
+major glycan classes and provides:
+
+*   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 archived on ModelArchive for reproducibility
+
+Useful resource if your AF3 ligand models appear stereochemically off.
+
+*   Paper: https://doi.org/10.1093/glycob/cwaf048
+*   ModelArchive: https://doi.org/10.5452/ma-af3glycan