ComplexMine is a small web based tool to find similar patterns in protein complexes. This application serves mainly as a small tech demo for database optimization technologies.
For a production ready feature-rich implementation users should refer to GeoMine on [https://proteins.plus].
This application uses PartitionCache to speed up database queries. For more information refer to [https://github.com/MPoppinga/PartitionCache]
- Setting up database.env
- Download and import dataset
- Download scripts for AlphaFold datasets are provided
Requirements
- PostgreSQL database (or compatible)
- Alternatively: MySQL or MariaDB, however in our tests PostgreSQL showed better performance
- Redis (or compatible)
- Python >= 3.9
For this demo application we use AlphaFold2 Data, however all PDB-style data sources should work.
For more information on the datasets in the download scripts see [https://alphafold.ebi.ac.uk]
Run for example
download_af_human.sh // (smaller dataset) or download_af_swiss_prot.sh // (larger dataset)
run importer
python importer.py --import_pdb --pdb_folder="data/af_db/"
python app.py --cachetype=redis
visit [http://localhost:5000]
(optional)
pcache-observer --db_backend=postgresql --db_env_file=database.env --cache_backend=redis --partition_key="complex_data_id" --db-name=alphafold_swissprot --long_running_query_timeout=300s
Protein Strucutres: AlphaFold Data Copyright (2022) DeepMind Technologies Limited.
This program is licensed under the GPLv3 license. See LICENSE for details.