Name
..
.attic
Media
additional_scripts
expected_outputs
inputs
outputs
01.00-How-to-Get-Started.ipynb
01.03-How-to-Get-Local-PyRosetta.ipynb
01.04-Notebooks-Python-Colab.ipynb
01.05-FAQ.ipynb
02.00-Introduction-to-PyRosetta.ipynb
02.01-Pose-Basics.ipynb
02.02-Working-with-Pose-Residues.ipynb
02.03-Accessing-PyRosetta-Documentation.ipynb
02.04-Getting-Spatial-Features-from-Pose.ipynb
02.05-Protein-Geometry.ipynb
02.06-Visualization-and-PyMOL-Mover.PyRosetta-ColabPyMOL-integration.ipynb
02.06-Visualization-and-PyMOL-Mover.ipynb
02.07-RosettaScripts-in-PyRosetta.ipynb
02.08-Visualization-and-pyrosetta.distributed.viewer.ipynb
03.00-Rosetta-Energy-Score-Functions.ipynb
03.01-Score-Function-Basics.ipynb
03.02-Analyzing-energy-between-residues.ipynb
03.03-Energies-and-the-PyMOLMover.ipynb
04.00-Introduction-to-Folding.ipynb
04.01-Basic-Folding-Algorithm.ipynb
04.02-Low-Res-Scoring-and-Fragments.ipynb
05.00-Structure-Refinement.ipynb
05.01-High-Res-Movers.ipynb
05.02-Refinement-Protocol.ipynb
06.00-Introduction-to-Packing-and-Design.ipynb
06.01-Side-Chain-Conformations-and-Dunbrack-Energies.ipynb
06.02-Packing-design-and-regional-relax.ipynb
06.03-Design-with-a-resfile-and-relax.ipynb
06.04-Protein-Design-2.ipynb
06.05-HBNet-Before-Design.ipynb
06.06-Introduction-to-Parametric-backbone-design.ipynb
06.07-Introduction-to-DeNovo-protein-design.ipynb
06.08-Point-Mutation-Scan.ipynb
07.00-Protein-Docking.ipynb
07.01-Fast-Fourier-Transform-Based-Docking-via-ZDOCK.ipynb
07.02-Docking-Moves-in-Rosetta.ipynb
08.00-Ligand-Docking-PyRosetta.ipynb
08.01-Ligand-Docking-XMLObjects.ipynb
08.02-Ligand-Docking-pyrosetta.distributed.ipynb
10.00-Working-With-Symmetry.ipynb
11.00-Working-With-Density.ipynb
12.00-Working-With-Antibodies.ipynb
12.01-RosettaAntibody-Framework-and-SimpleMetrics.ipynb
12.02-RosettaAntibodyDesign-RAbD.ipynb
13.00-RosettaCarbohydrates-Working-with-Glycans.ipynb
13.01-Glycan-Trees-Selectors-and-Movers.ipynb
13.02-Glycan-Modeling-and-Design.ipynb
14.00-RNA-Basics.ipynb
15.00-Modeling-Membrane-Proteins.ipynb
15.01-Accounting-for-the-lipid-bilayer.ipynb
15.02-Membrane-Protein-ddG-of-mutation.ipynb
16.00-Running-PyRosetta-in-Parallel.ipynb
16.01-PyData-ddG-pssm.ipynb
16.02-PyData-miniprotein-design.ipynb
16.03-GNU-Parallel-Via-Slurm.ipynb
16.04-dask.delayed-Via-Slurm.ipynb
16.05-Ligand-Docking-dask.ipynb
16.06-PyRosettaCluster-Simple-protocol.ipynb
16.07-PyRosettaCluster-Reproduce-simple-protocol.ipynb
16.08-PyRosettaCluster-Multiple-protocols.ipynb
16.09-PyRosettaCluster-Multiple-decoys.ipynb
16.10-PyRosettaCluster-Ligand-params.ipynb
A.00-Appendix-A.ipynb
B.00-Appendix-B.ipynb
C.00-Appendix-C.ipynb
D.00-Appendix-D.ipynb
index.ipynb
toc.ipynb
environment.yml
index.md
toc.md