This workshop walks through the process of preparing a simple protein + ligand system for molecular dynamics simulation:
- Using tools like Alphafold3 and Boltz2 to generate models for the protein/ligand complex.
- Adding hydrogen atoms to the models - fixing the ionization states of titratable groups.
- Creating a solvent environment - adding ions and water boxes.
- Conversion into file formats ready for MD simulation packages.
This training course is deployed on the CCPBioSim website via our cloud infrastructure, however you can deploy on your own machine with docker.
Pull the container from our repository::
docker pull ghcr.io/ccpbiosim/protein-preparation-workshop:latest
In our containers we are using the JupyterHub default port 8888, so you should forward this port when deploying locally::
docker run -p 8888:8888 ghcr.io/ccpbiosim/protein-preparation-workshop:latest
Workshop Content Authors:
- Charlie Laughton
- Hima Bindu Koli
- Jas Kalayan
Please direct all questions and feedback to Charlie Laughton