AlphaCharges
𝛂Charges: A tool for the quick calculation of partial atomic charges for protein structures from AlphaFold DB
Install / Use
/learn @sb-ncbr/AlphaChargesREADME
αCharges is a web application for the calculation of partial atomic charges on protein structures predicted by the AlphaFold2 algorithm and deposited in the AlphaFoldDB database. The charges are computed by the SQE+qp empirical method, which quality is comparable to quantum mechanical charge calculation approaches. Before computation of the charges, αCharges protonates the input protein structures by PROPKA3. The details about the methodology and usage are described in the manual. This website is free and open to all users and there is no login requirement.
How to run
To run AlphaCharges locally, you will need to have Python 3.12 and pip installed.
Then, clone project and install the project dependencies by running:
$ cd /opt
$ git clone https://github.com/sb-ncbr/AlphaCharges
$ sudo python3.12 -m venv venv
$ . venv/bin/activate
$ pip install -r AlphaCharges/requirements.txt
Run the project by running the following command inside the virtual environment:
(venv) $ cd /opt/Alphacharges/app
(venv) $ export FLASK_APP=routes.py
(venv) $ flask run
and point your browser to localhost:5000/.
How to cite
If you found AlphaCharges helpful, please cite: Schindler, O., Berka, K., Cantara, A., Křenek, A., Tichý, D., Raček, T., & Svobodová, R. (2023). αCharges: Partial atomic charges for AlphaFold structures in high quality. Nucleic Acids Research.
License
MIT
