Re-Glyco is a tool we designed to restore the missing glycosylation on glycoproteins deposited in the RCSB PDB or in the EBI-EMBL AlphaFold protein structure database. To get started, upload your protein structure file or choose a pre-existing AlphaFold or PDB structure, and let Re-Glyco do the rest! Currently supported function includes :

• N-GlcNAcylation
• O-GalNAcylation
• O-GlcNAcylation
• O-Fucosylation
• O-Mannosylation
• O-Glucosylation
• O-Xylosylation
• C-Mannosylation

This tool is currently hosted under GlycoShape project

sudo apt install build-essential
conda create -n reglyco python=3.12
conda activate reglyco
conda install conda-forge::gromacs 
pip install -r requirements.txt

curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
rustup update

cd glycors
maturin develop --release

Modify the config.py to locate the GlycoShape Database directory.

gunicorn -w 4 api:app --timeout 900

if you want to run on different port

gunicorn -w 4 api:app --timeout 1500 -b 127.0.0.1:8001 

The current version of Re-Glyco only has backend API service which can be used by GlycoShape Website code of the frontend website is here.

You can also use python script to access the API upload your pdb file and glycosylate it, a dummy code is provided as demo.py in this repo.

Once the API is running locally at your desired port. change the API_BASE_URL = "https://glycoshape.org" in demo.py to "http://127.0.0.1:8000"

and run using

python demo.py

This will upload the pdb to the API and will produced glycosylated structures can be found at output folder or temp_files.

It can take upto 5 minute for a job.

All of the data provided is freely available for academic use under Creative Commons Attribution 4.0 (CC BY-NC-ND 4.0 Deed) licence terms. Please contact us at [email protected] for Commercial licence. If you use this resource, please cite the following papers:

Callum M Ives and Ojas Singh et al. Restoring Protein Glycosylation with GlycoShape bioRxiv (2023).

• CLI interface
• Density fitting
• Fitness function with Non-bonded interaction.