Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design

View the Project on GitHub RosettaCommons/PyRosetta.notebooks

PyRosetta Workshops

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.

Table of Contents

Keyword Index

Chapter 1.0 How to Get Started

Chapter 2.0 Introduction to PyRosetta

Chapter 3.0 Rosetta Energy Score Functions

Chapter 4.0 Introduction to Folding

Chapter 5.0 Structure Refinement

Chapter 6.0 Packing & Design

Chapter 7.0 Docking

Chapter 8.0 Ligand Refinement in PyRosetta (a.k.a. High-Resolution Local Docking) Using the ligand.wts Scorefunction

Chapter 10.0 Working With Symmetry

Chapter 11.0 Working With Density

Chapter 12.0 Working With Antibodies

Chapter 13.0 RosettaCarbohydrates

Chapter 14.0 RNA in PyRosetta

Chapter 15.0 Modeling Membrane Proteins

Chapter 16.0 Running Rosetta in Parallel

Appendix A. Command Reference

Appendix B. Residue Parameter Files

Appendix C. Cleaning pdb files