RingPDB

RingPDB is an interactive web application for exploring ring conformations in experimentally determined protein structures. It allows users to search, filter, and visualise rings and their conformations in non-standard residues deposited in the Protein Data Bank (PDB).

Website: https://ringpdb.biodata.ceitec.cz

Related publication

RingPDB builds on a previous workflow for the conformational analysis of rings in ligands:

Analysis of cyclohexane, cyclopentane, and benzene conformations in ligands for PDB X-ray structures using the Hill-Reilly approach by Bučeková G, Doshchenko V, Svoboda T, Porubská J, Chareshneu A, Raček T, et al. Journal of Cheminformatics (2026).

DOI: 10.1186/s13321-026-01154-0

How to run

Dataset management with Git LFS

Large dataset files are managed using Git Large File Storage (Git LFS). Make sure Git LFS is installed and initialized before cloning or updating the repository.

Development

docker compose -f ./docker/docker-compose.yml up --build --watch

Production on local machine

echo "VITE_API_URL=/api" > frontend/.env.production.local
docker compose -f ./docker/docker-compose-production-local.yml up --build

Production

docker compose -f ./docker/docker-compose-production-local.yml -f ./docker/docker-compose.production.yml up -d --build

Adding new data from the workflow

When updating the dataset, two files generated by the workflow (inside web folder) must be manually updated in the web application repository:

rings.parquet -> api/data/rings.parquet

stats.json -> frontend/src/content/stats.json