toc.md

PyRosetta

Chapter 1.0 How to Get Started

• Students
• Instructors

• Links
  • PyRosetta package

1.1 PyRosetta Google Drive Setup

1.2 PyRosetta Google Drive Usage Example

1.3 How to Get PyRosetta on Your Personal Computer

• Download the main necessary packages to work locally on your machine
  • Python 3.6 (and preferably IPython for tab-completion)
  • PyMOL
  • PyRosetta-3.6.Release

Chapter 2.0 Introduction to PyRosetta

2.1 Pose Basics

• Loading in a PDB File ##
• What is a Pose?
  • Exercise 1: Inspecting pose sequences
  • Bonus Exercise 1: Identifying differences in sequences

2.2 Working with Pose residues

• Exercise 2: Residue objects

2.3 Accessing PyRosetta Documentation

• Exercise 3: Python Object Help
• Exercise 4: Some residue commands

2.4 Getting spatial features from a Pose

• References

2.5 Protein Geometry

• Rosetta Database Files
  • Exercise 5: Calculating psi angle
• Manipulating Protein Geometry

2.6 Visualization with the PyMOLMover

• Exercise 7: Visualizing changes in backbone angles
• Additional Exercises ##
  • Analyzing Amino Acid Patterns
  • Active Site Residues
• Answers
  • Exercise 6
• References

• Links
  • Ramachandran plot
  • Richardson's Anatomy and Taxonomy of Protein Structure

2.7 RosettaScripts in PyRosetta

• Running Whole Protocols via RosettaScriptsParser
• Running via XMLObjects and strings
• Constructing Rosetta objects using XMLObjects
  • Constructing from single section

2.8 Visualization and pyrosetta.distributed.viewer

- [Available `viewer` objects:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.08-Visualization-and-pyrosetta.distributed.viewer.ipynb#Available-`viewer`-objects:)
- [Available `viewer.presets` objects:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.08-Visualization-and-pyrosetta.distributed.viewer.ipynb#Available-`viewer.presets`-objects:)
- [`viewer` objects contain docstrings as user documentation:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.08-Visualization-and-pyrosetta.distributed.viewer.ipynb#`viewer`-objects-contain-docstrings-as-user-documentation:)
- [`viewer.presets` objects contain docstrings as brief descriptions of each preset visualization](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/02.08-Visualization-and-pyrosetta.distributed.viewer.ipynb#`viewer.presets`-objects-contain-docstrings-as-brief-descriptions-of-each-preset-visualization)

Chapter 3.0 Rosetta Energy Score Functions

3.1 Score Function Basics

• Practice: List the terms in the energy function and their relative weights
• Custom energy functions
• Energy Breakdown

• Links
  • documentation

3.2 Practice: Analyzing energy between residues

3.3 Energies and the PyMOL Mover

• References

Chapter 4.0 Introduction to Folding

4.1 Basic Folding Algorithm

• Building the Pose
• Building A Basic de Novo Folding Algorithm
  • Step 1: Random Move
  • Step 2: Scoring Move
  • Step 3: Accepting/Rejecting Move
  • Step 4: Execution
  • Exercise 1: Comparing to Alpha Helices
  • Exercise 2: Optimizing Algorithm

4.2 Low-Res Scoring and Fragments

• Low-Resolution (Centroid) Scoring
  • SwitchResidueTypeSetMover
  • Exercise 1: Centroid Folding Algorithm
  • Note about Movers
• Protein Fragments
  • Using FragmentMover and MoveMap
  • Exercise 2: Fragment Folding Algorithm
  • Programming Exercises

Chapter 5.0 Structure Refinement

5.1 High-Resolution Movers

• Small and Shear Moves
  • Test your mover by applying it to your pose
  • Comparing small and shear movers
• Minimization Moves
• Monte Carlo Object
• Trial Mover
• Sequence and Repeat Movers

5.2 Refinement Protocol

• Programming Exercises
• Thought Questions

Chapter 6.0 Packing & Design

6.1 Side Chain Conformations and Dunbrack Energies

6.2 Packing and Relax

• Imports
• Intitlialization
• Import and copy pose
• Setup a Normal TaskFactory
• Setup The Packer
• Regional Packing
  • Restrict to our selection
  • Reset the pose
• Design
  • Set and Run
• Relax
  • Regional Relax
  • Regional Relax - Classic

6.3 Protein Design with a Resfile and FastRelax

• Overview
  • Initialize PyRosetta
• Design strategy:
  • Analysis

6.4 Protein Design 2

• Initialize PyRosetta
• Design strategy
• Design Challenge:

6.5 HBNet Before Design

• Setting Designable Residues:
• Running HBNet
• Finishing Design:
• We made it...?
• But wait, there's more??
• Advice for using this in the wild
• Thought Question

6.6 De Novo Parametric Backbone Design

• Overview
• Changing omega0
• MakeBundle Mover in PyRosetta
• Conclusion
• References:

6.7 De Novo Protein Design with PyRosetta

• Design Strategy
• De Novo Protein Design
• Analysis:

Chapter 7.0 Docking

7.1 Fast Fourier Transform Based Docking via ZDOCK

7.2 Docking Moves in Rosetta

• Rigid-body transformations and Fold Trees
• RigidBody Movers
• Low-Resolution Docking via RosettaDock
• Job Distributor
• High-Resolution Docking
• Docking Funnel
• Programming Exercises

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

7.4 Global Ligand Docking using XMLObjects Using the ref2015.wts Scorefunction

7.5 GALigandDock Protocol with pyrosetta.distributed Using the beta_cart.wts Scorefunction

- [Inspect the scores for the `GALigandDock` trajectories:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/07.05-Ligand-Docking-pyrosetta.distributed.ipynb#Inspect-the-scores-for-the-`GALigandDock`-trajectories:)
- [Now that we have performed `GALigandDock`, we can plot the ligand binding energy landscape:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/07.05-Ligand-Docking-pyrosetta.distributed.ipynb#Now-that-we-have-performed-`GALigandDock`,-we-can-plot-the-ligand-binding-energy-landscape:)

Chapter 9.0 Working With Symmetry

• Creating a SymDef file
• Setup a Symmetrized Pose
• Running Protocols with Symmetry
• Conclusions

Chapter 10.0 Working With Density

• Creating a Density Map
• Setup for Density Scoring
• Conclusion

Chapter 11.0 Working With Antibodies

• Overview
• IgG
• CDRs
• Antibody Numbering Schemes

11.1 RosettaAntibody Framework

• Imports
• Intitlialization
• Import and copy pose
• AntibodyInfo
• Basic AntibodyInfo Access
  • AntibodyEnumManager
  • CDR Clusters
  • Numbering Scheme Translation
  • Sequence
  • Other AntibodyInfo functions
  • AntibodyInfo Deprecated Functions
• Antibody Util and SimpleMetrics
  • Function: select_epitope_residues()
  • SasaMetric, TotalEnergyMetric, SelectedResiduesPyMOLMetric
  • PerResidueSasaMetric
• Other Useful Antibody Tools
  • AntibodyRegionSelector
  • Other
• References

• Links
  • Side Chain Conformations and Dunbrack Energies
  • Contents
  • Index
  • Protein Design with a Resfile and FastRelax

11.2 RosettaAntibodyDesign

• Imports
• Intitlialization
  • Tut A1. Sequence Design
  • Tut A2. Graft Design
  • Tut A3. Basic De-novo run
  • Tut A4. RAbD Framework Components
  • Challenge: Custom Design Protocol in code
• Tutorial B: Optimizing Interface Energy (opt-dG)
  • Tut B2. Optimizing Interface Energy and Total Score (opt-dG and opt-E)
• Tutorial C: Towards DeNovo Design: Integrated Dock/Design
  • Tut C2. Auto Epitope Constraints
  • Tut C3. Specific Residue Epitope Constraints
• Tutorial D: Advanced Settings and CDR Instruction File Customization
  • Tut D2. Dissallow AAs and the Resfile
  • Tut D3. Mintype
  • Tut D4. Framework Design
  • Tut D5. H3 Stem, kT, and Sequence variablility.

• Links
  • Rosetta Antibody Design (RAbD): A General Framework for Computational Antibody Design, PLOS Computational Biology, 4/27/2018
  • recent clustering
  • PyIgClassify Server
  • Side Chain Conformations and Dunbrack Energies
  • Contents
  • Index
  • Protein Design with a Resfile and FastRelax

Chapter 12.0 RosettaCarbohydrates

• Carbohydrate Chemistry Background
• Initialization
• Creating Saccharides from Sequence
  • Anomers
  • Linear Oligosaccharides & IUPAC Sequences
  • General Residue Information
• Exploring Carbohydrate Structure
  • Creating Saccharides from a PDB file
  • RingConformers
• Modified Sugars, Branched Oligosaccharides, & .pdb File LINK Records
• N- and O-Linked Glycans
  • Glycosylation by function
• Conclusion

12.1 RosettaCarbohydrates: Trees, Selectors and Movers

• Imports
• Intitlialization
• Object Exploration: GlycanTreeSet, CarbohydrateInfo, and the GlycanInfoMover - GlycanTree and GlycanNode
  • CarbohydrateInfo
• GlycanInfoMover
  • Branched Connections
  • MoveMapFactory vs MoveMap creation
• Glycan Residue Selectors - All Carbohydrates - Branch Selection
  • GlycanLayerSelector
  • GlycanSequonSelector
  • RandomGlycanFoliageSelector
• Glycan Movers
  • Correcting Structures
    • IdealizeAnomericHydrogens
    • RingPlaneFlipMover
  • Glycosylation
  • BB Sampling
    • BBSampler: SugarBBSampler
• Conclusion

• Links
  • Working With Glycans

12.2 RosettaCarbohydrates: Modeling and Design

    - [A1.2 Design using the `N[^P][T]` motif](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.02-Glycan-Modeling-and-Design.ipynb#A1.2-Design-using-the-`N[^P][T]`-motif)
- [A2. Adding a man5 glycan:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.02-Glycan-Modeling-and-Design.ipynb#A2.-Adding-a-man5-glycan:)
- [A3. Modeling glycans](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/12.02-Glycan-Modeling-and-Design.ipynb#A3.-Modeling-glycans)

• Tutorial B: Using Glycan Density
  • B1. Calculating Density Fit
  • B2. Refinement into density
  • B3. Denovo building into Density

• Links
  • Working With Glycans

Chapter 13.0 RNA in PyRosetta

• References
• Introduction
• Exploring geometry for RNA ##
• Scoring RNA poses ##
• Manipulating RNA poses ##
• Elements of RNA Structure Prediction
  • Generating an ideal A-form Helix
  • RNA Fragments
  • Minimizing Structures with RNA
• Additional Exercises
  • Post-mortem
  • FAR + FAR = FARFAR
• RNA Structure Prediction Protocol

• Links
  • Fragment Assembly of RNA with Full Atom Refinement

Chapter 15.0 Running Rosetta in Parellel

• Links
  • Integration of the Rosetta Suite with the Python Software Stack via reproducible packaging and core programming interfaces for distributed simulation

15.1 Distributed analysis example: exhaustive ddG PSSM

• Create test pose, initialize rosetta and pack
• Perform exhaustive point mutation and pack
• Job distribution via multiprocessing
• Job distribution via dask
• Analysis of delta score

• Links
  • Integration of the Rosetta Suite with the Python Software Stack via reproducible packaging and core programming interfaces for distributed simulation

15.2 Distributed computation example: miniprotein design

• Links
  • Integration of the Rosetta Suite with the Python Software Stack via reproducible packaging and core programming interfaces for distributed simulation

15.3 Example of Using PyRosetta with GNU Parallel

- [1. Parallelize script in an interactive session:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/15.03-GNU-Parallel-Via-Slurm.ipynb#1.-Parallelize-script-in-an-interactive-session:)
- [2. Parallelize script on a high-performance computing cluster with Slurm scheduling (non-interactive submission):](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/15.03-GNU-Parallel-Via-Slurm.ipynb#2.-Parallelize-script-on-a-high-performance-computing-cluster-with-Slurm-scheduling-(non-interactive-submission):)
- [3. Submit jobs individually to the SLURM scheduler:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/15.03-GNU-Parallel-Via-Slurm.ipynb#3.-Submit-jobs-individually-to-the-SLURM-scheduler:)

15.4 Examples Using the dask Module

- [We can make use of the `dask` library to parallelize code](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/15.04-dask.delayed-Via-Slurm.ipynb#We-can-make-use-of-the-`dask`-library-to-parallelize-code)
- [Consider the following example that runs within this Jupyter notebook kernel just fine but could be parallelized:](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/15.04-dask.delayed-Via-Slurm.ipynb#Consider-the-following-example-that-runs-within-this-Jupyter-notebook-kernel-just-fine-but-could-be-parallelized:)

15.5 Part I: Parallelized Global Ligand Docking with pyrosetta.distributed