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 PyRosetta Google Drive Setup
- 1.2 PyRosetta Google Drive Usage Example
- 1.3 How to Get PyRosetta on Your Personal Computer
- 1.4 Jupyter Notebooks, Python, and Google Colaboratory
- 1.5 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 RosettaScripts in PyRosetta
- 2.8 Visualization and
pyrosetta.distributed.viewer
- 3.1 Score Function Basics
- 3.2 Practice: Analyzing energy between residues
- 3.3 Energies and the PyMOL Mover
- 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
Chapter 8.0 Ligand Refinement in PyRosetta (a.k.a. High-Resolution Local Docking) Using the ligand.wts Scorefunction
- 8.1 Global Ligand Docking using
XMLObjectsUsing theref2015.wtsScorefunction - 8.2
GALigandDockProtocol withpyrosetta.distributedUsing thebeta_cart.wtsScorefunction
- 13.1 RosettaCarbohydrates: Trees, Selectors and Movers
- 13.2 RosettaCarbohydrates: Modeling and Design
- 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
daskModule - 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