Welcome to PyRosetta!

PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling suite. It enables users to design their own custom molecular modeling algorithms using Rosetta sampling methods and energy functions.

The Jupyter Notebooks below provide an introduction to the fundmamental principles and tools for using PyRosetta. The Notebooks can be viewed directly in nbviewer. To execute any of the notebooks either locally or in Google Colaboratory, please see Chapter 1 for setup instructions.

Many of the workshops have been adapted from the book The PyRosetta Interactive Platform for Protein Structure Prediction and Design: PyRosetta4 Update by Jeffrey Gray, Sidhartha Chaudhury, Sergey Lyskov, and Jason Labonte (Amazon). Other Rosetta developers have also lent their various areas of expertise to help create workshops for this series. Additional contributions to our open-source repository are always welcomed. To learn more about this project, check out our preprint.

• 1.1 How to Get PyRosetta on Your Personal Computer
• 1.2 Jupyter Notebooks, Python, and Google Colaboratory
• 1.3 Frequently Asked Questions/Troubleshooting Tips

• 2.1 Pose Basics
• 2.2 Working with Pose residues
• 2.3 Accessing PyRosetta Documentation
• 2.4 Getting spatial features from a Pose
• 2.5 Protein Geometry
• 2.6 Visualization with the PyMOLMover
• 2.7 Visualization with the PyMOLMover, PyRosetta ColabPyMOL integration
• 2.8 RosettaScripts in PyRosetta
• 2.9 Visualization and pyrosetta.distributed.viewer

• 3.1 Score Function Basics
• 3.2 Practice: Analyzing energy between residues
• 3.3 Energies and the PyMOL Mover

• 4.1 Basic Folding Algorithm
• 4.2 Low-Res Scoring and Fragments

• 5.1 High-Resolution Movers
• 5.2 Refinement Protocol

• 6.1 Side Chain Conformations and Dunbrack Energies
• 6.2 Packing and Relax
• 6.3 Protein Design with a Resfile and FastRelax
• 6.4 Protein Design 2
• 6.5 HBNet Before Design
• 6.6 De Novo Parametric Backbone Design
• 6.7 De Novo Protein Design with PyRosetta
• 6.8 Point Mutation Scan

• 7.1 Fast Fourier Transform Based Docking via ZDOCK
• 7.2 Docking Moves in Rosetta

• 8.1 Global Ligand Docking using XMLObjects Using the ref2015.wts Scorefunction
• 8.2 GALigandDock Protocol with pyrosetta.distributed Using the beta_cart.wts Scorefunction

• 9.1 Using Rosetta Gen KIC

• 12.1 RosettaAntibody Framework
• 12.2 RosettaAntibodyDesign

• 13.1 RosettaCarbohydrates: Trees, Selectors and Movers
• 13.2 RosettaCarbohydrates: Modeling and Design

• 15.1 Setting up a membrane protein in the bilayer
• 15.2 Predicting the ∆∆G of single point mutations

• 16.1 Distributed analysis example: exhaustive ddG PSSM
• 16.2 Distributed computation example: miniprotein design
• 16.3 Example of Using PyRosetta with GNU Parallel
• 16.4 Examples Using the dask Module
• 16.5 Part I: Parallelized Global Ligand Docking with pyrosetta.distributed
• 16.6 PyRosettaCluster Tutorial 1A. Simple protocol
• 16.7 PyRosettaCluster Tutorial 1B. Reproduce simple protocol
• 16.8 PyRosettaCluster Tutorial 2. Multiple protocols
• 16.9 PyRosettaCluster Tutorial 3. Multiple decoys
• 16.10 PyRosettaCluster Tutorial 4. Ligand params
• 16.11 PyRosettaCluster Tutorial 5. Foundry