mol_model_course_2023

Workshop: Introduction to Rosetta

Description

• We will outline basic methods of working with Rosetta protein modeling suite using pyRosetta.
• Duration: 90 minutes
• Objectives: be able to
  • Understand how to setup modeling with Rosetta
  • Understand how to setup protein folding simulations
  • Understand how to setup basic protein design simulations

Jupyter notebooks

• We follow this tutorial.
• The github repo is here
• Notebooks in Google Drive folder here

Required software and resources

• Easiest way is to use Google Colab Google Drive - see tutorial for initialization instructions. However, this will require a lengthy download.
• Or you need local access to a Jupyter notebook evironment with pyRosetta installed, see here
• Or use Newton cluster pRosetta conda environment.

Learning resources

• pyRosetta tutorials

Assignments

Take a protein of interest:

1. Analyze energy between any two residues, output various energy terms.
2. Take an arbitrary sequence of 10 amino acids. Try to do folding. Explore different lowest conformations depeding on the number of Monte-Carlo steps. Visualize results.

Troubleshooting

• Consult with the seminar protocol/recording
• Ask questions in Slack