# PyRosetta.notebooks

**Repository Path**: philloidin/PyRosetta.notebooks

## Basic Information

- **Project Name**: PyRosetta.notebooks
- **Description**: Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design
- **Primary Language**: Unknown
- **License**: MIT
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2021-08-26
- **Last Updated**: 2021-08-26

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README


[//]: # (DO NOT EDIT. README.md is generated by nbpages. Make changes templates/README.md.jinja.)
# 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](https://www.amazon.com/PyRosetta-Interactive-Platform-Structure-Prediction-ebook/dp/B01N21DRY8)). 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](https://github.com/RosettaCommons/PyRosetta.notebooks) are always welcomed. To learn more about this project, check out our [preprint](https://www.preprints.org/manuscript/202002.0097/v1).


### [Table of Contents](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/toc.ipynb?flush=true)
### [Keyword Index](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/index.ipynb?flush=true)

### [Chapter 1.0 How to Get Started](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/01.00-How-to-Get-Started.ipynb)
- [1.1 PyRosetta Google Drive Setup](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/01.01-PyRosetta-Google-Drive-Setup.ipynb)
- [1.2 PyRosetta Google Drive Usage Example](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/01.02-PyRosetta-Google-Drive-Usage-Example.ipynb)
- [1.3 How to Get PyRosetta on Your Personal Computer](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/01.03-How-to-Get-Local-PyRosetta.ipynb)
- [1.4 Jupyter Notebooks, Python, and Google Colaboratory](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/01.04-Notebooks-Python-Colab.ipynb)
- [1.5 Frequently Asked Questions/Troubleshooting Tips](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/01.05-FAQ.ipynb)

### [Chapter 2.0 Introduction to PyRosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.00-Introduction-to-PyRosetta.ipynb)
- [2.1 Pose Basics](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.01-Pose-Basics.ipynb)
- [2.2 Working with Pose residues](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.02-Working-with-Pose-Residues.ipynb)
- [2.3 Accessing PyRosetta Documentation](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.03-Accessing-PyRosetta-Documentation.ipynb)
- [2.4 Getting spatial features from a Pose](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.04-Getting-Spatial-Features-from-Pose.ipynb)
- [2.5 Protein Geometry](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.05-Protein-Geometry.ipynb)
- [2.6 Visualization with the `PyMOLMover`](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.06-Visualization-and-PyMOL-Mover.ipynb)
- [2.7 RosettaScripts in PyRosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.07-RosettaScripts-in-PyRosetta.ipynb)
- [2.8 Visualization and `pyrosetta.distributed.viewer`](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.08-Visualization-and-pyrosetta.distributed.viewer.ipynb)

### [Chapter 3.0 Rosetta Energy Score Functions](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/03.00-Rosetta-Energy-Score-Functions.ipynb)
- [3.1 Score Function Basics](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/03.01-Score-Function-Basics.ipynb)
- [3.2 Practice: Analyzing energy between residues](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/03.02-Analyzing-energy-between-residues.ipynb)
- [3.3 Energies and the PyMOL Mover](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/03.03-Energies-and-the-PyMOLMover.ipynb)

### [Chapter 4.0 Introduction to Folding](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/04.00-Introduction-to-Folding.ipynb)
- [4.1 Basic Folding Algorithm](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/04.01-Basic-Folding-Algorithm.ipynb)
- [4.2 Low-Res Scoring and Fragments](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/04.02-Low-Res-Scoring-and-Fragments.ipynb)

### [Chapter 5.0 Structure Refinement](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/05.00-Structure-Refinement.ipynb)
- [5.1 High-Resolution Movers](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/05.01-High-Res-Movers.ipynb)
- [5.2 Refinement Protocol](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/05.02-Refinement-Protocol.ipynb)

### [Chapter 6.0 Packing & Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.00-Introduction-to-Packing-and-Design.ipynb)
- [6.1 Side Chain Conformations and Dunbrack Energies](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.01-Side-Chain-Conformations-and-Dunbrack-Energies.ipynb)
- [6.2 Packing and Relax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.02-Packing-design-and-regional-relax.ipynb)
- [6.3 Protein Design with a Resfile and FastRelax](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.03-Design-with-a-resfile-and-relax.ipynb)
- [6.4 Protein Design 2](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.04-Protein-Design-2.ipynb)
- [6.5 HBNet Before Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.05-HBNet-Before-Design.ipynb)
- [6.6 *De Novo* Parametric Backbone Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.06-Introduction-to-Parametric-backbone-design.ipynb)
- [6.7 *De Novo* Protein Design with PyRosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.07-Introduction-to-DeNovo-protein-design.ipynb)
- [6.8 **Point Mutation Scan**](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/06.08-Point-Mutation-Scan.ipynb)

### [Chapter 7.0 Docking](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/07.00-Protein-Docking.ipynb)
- [7.1 Fast Fourier Transform Based Docking via ZDOCK](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/07.01-Fast-Fourier-Transform-Based-Docking-via-ZDOCK.ipynb)
- [7.2 Docking Moves in Rosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/07.02-Docking-Moves-in-Rosetta.ipynb)

### [Chapter 8.0 Ligand Refinement in PyRosetta (a.k.a. High-Resolution Local Docking) Using the `ligand.wts` Scorefunction](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/08.00-Ligand-Docking-PyRosetta.ipynb)
- [8.1 Global Ligand Docking using `XMLObjects` Using the `ref2015.wts` Scorefunction](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/08.01-Ligand-Docking-XMLObjects.ipynb)
- [8.2 `GALigandDock` Protocol with `pyrosetta.distributed` Using the `beta_cart.wts` Scorefunction](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/08.02-Ligand-Docking-pyrosetta.distributed.ipynb)

### [Chapter 10.0 Working With Symmetry](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/10.00-Working-With-Symmetry.ipynb)

### [Chapter 11.0 Working With Density](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/11.00-Working-With-Density.ipynb)

### [Chapter 12.0 Working With Antibodies](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.00-Working-With-Antibodies.ipynb)
- [12.1 RosettaAntibody Framework](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.01-RosettaAntibody-Framework-and-SimpleMetrics.ipynb)
- [12.2 RosettaAntibodyDesign](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.02-RosettaAntibodyDesign-RAbD.ipynb)

### [Chapter 13.0 RosettaCarbohydrates](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.00-RosettaCarbohydrates-Working-with-Glycans.ipynb)
- [13.1 RosettaCarbohydrates: Trees, Selectors and Movers](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.01-Glycan-Trees-Selectors-and-Movers.ipynb)
- [13.2 RosettaCarbohydrates: Modeling and Design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/13.02-Glycan-Modeling-and-Design.ipynb)

### [Chapter 14.0 RNA in PyRosetta](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/14.00-RNA-Basics.ipynb)

### [Chapter 15.0 Modeling Membrane Proteins](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/15.00-Modeling-Membrane-Proteins.ipynb)
- [15.1 Setting up a membrane protein in the bilayer](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/15.01-Accounting-for-the-lipid-bilayer.ipynb)
- [15.2 Predicting the ∆∆G of single point mutations](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/15.02-Membrane-Protein-ddG-of-mutation.ipynb)

### [Chapter 16.0 Running Rosetta in Parallel](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.00-Running-PyRosetta-in-Parallel.ipynb)
- [16.1 Distributed analysis example: exhaustive ddG PSSM](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.01-PyData-ddG-pssm.ipynb)
- [16.2 Distributed computation example: miniprotein design](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.02-PyData-miniprotein-design.ipynb)
- [16.3 Example of Using PyRosetta with GNU Parallel](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.03-GNU-Parallel-Via-Slurm.ipynb)
- [16.4 Examples Using the `dask` Module](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.04-dask.delayed-Via-Slurm.ipynb)
- [16.5 Part I: Parallelized Global Ligand Docking with `pyrosetta.distributed`](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.05-Ligand-Docking-dask.ipynb)
- [16.6 PyRosettaCluster Tutorial 1A. Simple protocol](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.06-PyRosettaCluster-Simple-protocol.ipynb)
- [16.7 PyRosettaCluster Tutorial 1B. Reproduce simple protocol](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.07-PyRosettaCluster-Reproduce-simple-protocol.ipynb)
- [16.8 PyRosettaCluster Tutorial 2. Multiple protocols](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.08-PyRosettaCluster-Multiple-protocols.ipynb)
- [16.9 PyRosettaCluster Tutorial 3. Multiple decoys](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.09-PyRosettaCluster-Multiple-decoys.ipynb)
- [16.10 PyRosettaCluster Tutorial 4. Ligand params](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/16.10-PyRosettaCluster-Ligand-params.ipynb)

### [Appendix A. Command Reference](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/A.00-Appendix-A.ipynb)

### [Appendix B. Residue Parameter Files](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/B.00-Appendix-B.ipynb)

### [Appendix C. Cleaning pdb files](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/C.00-Appendix-C.ipynb)

### [Appendix D. Links to Online Help](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/D.00-Appendix-D.ipynb)