Demos listed by keyword

Tutorials

Tutorials intended as a gentle introduction to Rosetta concepts, and using common functionality of Rosetta.

List of Tutorials

Demos

These demos are designed to guide users through sample procedures in computational modeling from the point of view of solving a specific problem.

Full input files for the demos are located in the demos/public/ directory of the Rosetta distribution.

Structure Prediction

Utilities

• fragment_picking: Standard fragment picking
• fragment_picking_for_cs_rosetta: Fragment Picking for CS-Rosetta

Loops

• comparative_modeling: Comparative Modeling: Single template modeling and loop building
• model_missing_loop: Model a Missing Loop
• stepwise_monte_carlo_protein_loop: StepWise Monte Carlo (example for protein loop)
• swa_protein_main: SWA Protein Main

Experimental Data

• abinitio_w_chemicalshift_noe: AbInitio Structure Prediction Using Chemical-Shift Generated Fragments and NOE Distance Restraints
• abinitio_w_chemicalshift_noe_rdc: AbInitio Structure Prediction Using Chemical-Shift Generated Fragments, NOE Distance Restraints and RDC Restraints
• abinitio_w_chemicalshift_only: AbInitio Structure Prediction Using Chemical-Shift Generated Fragments
• hrf_rosetta: Rescoring Rosetta Models using low resolution HRF Mass Spectrometry Data
• structure_refinement: Rosetta tools for structure determination in density

Peptides

• refinement_of_protein_peptide_complex_using_FlexPepDock: Refinement of peptide-protein complexes using FlexPepDock refinement

Nucleic Acids

• cs_rosetta_rna: CS-Rosetta RNA: Using chemical shifts with RNA structure refinement
• rna_assembly: RNA Assembly

Denovo

• rnp_structure_prediction: Structure prediction of an RNA-protein complex
• stepwise_monte_carlo_mini_protein: StepWise Monte Carlo to build a small protein

General

• abinitio: AbInitio: Predict structure from sequence
• backrub_seqtol: Backrub Sequence Tolerance
• broker_ubq: Topology Broker - AbInitio with a given beta strand topology
• confchangemover_membrane: ConfChangeMover for membrane proteins
• confchangemover_soluble: ConfChangeMover for soluble proteins
• fixbb: Demo for the fixbb application
• floppy_tail: Floppy Tail Demo
• gps_rosetta_pcs_nmr_constraints: Capturing Conformational States in Proteins Using Pseudocontact Shifts (PCS)
• homology_modeling_threading_basic: Basic Homology Modeling Demo
• relax_a_large_structure: Relax a Large Structure
• stepwise_enumerative_assembly: Stepwise Enumerative Assembly

Design

Utilities

• favor_native_residue: Favor Native Residue

Loops

• design_with_flex_loops: Design with flexible loops
• next_generation_kic: Next Generation KIC

Interfaces

• anchored_design: Anchored Design
• beta_strand_homodimer_design: β-Strand Homodimer Design
• design_raf_rac_interface: Design the Rac/Raf interface

Enzymes

• enzyme_design: Enzyme Design Demo

Peptides

• threefold_symmetric_peptide_design: Designing Threefold-Symmetric Meso-Sized Polypeptides With Threefold-Symmetric Cross-linkers

Noncanonicals

• design_with_ncaa: Design with non-canonical amino acids (NCAA)

Metals

• zinc_site_redesign: Zinc Site Redesign

Stability Improvement

• ts_mutant: Temperature-Sensitive Mutation Prediciton
• vip: Rosetta VIP: Void Indentification and Packing

General

• broker_domain_insertion: Toplogy Broker - Domain Insertion Protocol Capture
• domain_insertion: Domain Insertion Demo
• fixbb_design: Demo for the fixbb application with design
• ideal_proteins: Design of Proteins with Ideal Topologies
• multi_state_desing_of_antibodies: Multistate Design of Antibodies
• supercharge: Supercharge: Reengineer proteins for high net surface charge

Analysis

Interfaces

• analyzing_interface_quality: Analyzing Interface Quality
• calculate_protein_protein_ddg: Calculate Protein Protein ΔΔG

General

• clustering: Clustering: Group similar decoys with the Rosetta cluster application.
• unfolded_state_energy_calculator: Instructions for Calculating Explicit Unfolded State Energies for Noncanonical Amino Acids

Utilities

General

• foldit_standalone: Foldit Standalone Protocol Capture
• optE: optE: Refit Rosetta reference energies
• prepare_pdb_for_rosetta_with_relax: Relax with all-heavy-atom constraints
• prepare_pdbs_for_rosetta: Prepare PDBs for Rosetta

Scripting Interfaces

Design

• rosetta_scripts_enzdes: Rosetta scripts: enzdes
• rosetta_scripts_flxbb_design: Flexible backbone design with RosettaScripts

Loops

• rosetta_scripts_LoopRemodel: Loop Remodel

Interfaces

• rosetta_scripts_pp-interfaceredesign: Protein protein interface design using rosetta scripts

Nucleic Acids

• rosetta_scripts_RosettaDNA: Rosetta scripts: Rosetta-DNA Demo

General

• rosetta_scripts: RosettaScripts example scripts

Loops

Design

• shortening_loops: Shortening loops in Rosetta

Membranes

• topology_broker_gpcr: Protocol Name:Loop Building for Membrane Proteins with Toplogy Broker

Nucleic Acids

• stepwise_monte_carlo_rna_loop: StepWise Monte Carlo of an RNA loop

General

• swa_protein_long_loop: SWA Protein Loop Long

Docking

Structure Prediction

• canonical_sampling_docking: Canonical Sampling for Protein-Protein Docking Refinement
• gpcr_model_dock: GPCR Model Dock Protocol Capture

Design

• doug_dock_design_min: Doug's DockDesignMinimize Demo

Analysis

• predict_eglinC_ddgs: Predict DDGs for the eglinC protein

Interfaces

• dock_with_user_defined_constraints: Docking with constraints
• replica_docking: Replica Docking

Experimental Data

• xl_driven_protein_docking: Crosslink Guided Protein-Protein Docking

Symmetry

• symmetric_docking_insulin_trimer_of_dimers: Symmetric Docking of Insulin Trimer of Dimers - Demo

Ligands

• darc: DARC Demo

Peptides

• flex_pep_dock_abinitio: FlexPepDock AbInitio Protocol Capture

General

• broker_snugdock: Toplogy Broker - SnugDock Protocol Capture

Interfaces

Design

• peptide_designs: Peptide Backbone and Sequence Design

General

• interface_design_demo: Interface Design Demo

Surfaces

Docking

• surface_docking_cpp: C++ RosettaSurface

Experimental Data

Structure Prediction

• cryo_em_tutorial: Modeling using low to medium resolution cryoEM data.
• molecular_replacement: Molecular Replacement Demo
• spin_labels: Spin Labels

General

• rasrec_evolutionary_restraints: RASREC Evolutionary Restraints

Membranes

Structure Prediction

• membrane_abinitio: Membrane ab initio modeling
• membrane_folding_tutorial: Membrane Protein Folding
• membrane_homology_modeling: Membrane Homology Modeling
• mp_relax: Membrane Relax
• original_mp_relax_menv_smooth: Membrane Relax with Menv_smooth Term

Analysis

• mp_span_from_pdb: Spanfile from PDB

Utilities

• mp_pymol_viewer: Visualizing Membranes in PyMOL

Docking

• mp_ddg: Membrane ΔΔG
• mp_dock: Membrane Protein-Protein Docking
• mp_symdock: Membrane Symmetric Protein-Protein Docking

Antibodies

Docking

• antibody_docking: Antibody Docking

Ligands

Structure Prediction

• rosettaligand_transform: RosettaLigand Transform

Utilities

• optimize_ligand_hydroxyl_hydrogens: Optimize Ligand Hydroxyl Hydrogens

Docking

• chemically_conjugated_docking: Chemically Conjugated Docking
• dock_protein_complex_with_ligand_xml: Dock protein complex with ligand
• hbs_design: HBS Design Demo
• ligand_dock_commandline: Ligand Dock Demo
• ligand_water_docking: Ligand-centric Water Docking

Interfaces

• relax_around_chemically_bound_ligand: Relax Around A Chemically Bound Ligand

Noncanonicals

• design_with_phosphoresidue: Design with Phosphoresidues

Peptides

Design

• beta_peptide_modeling: Beta-3-peptide design
• oop_design: Oop Design: Design with oligooxopiperazine helix mimetics

Docking

• abinitio_fold_and_dock_of_peptides_using_flexpepdock: AbInitio fold-and-dock of peptides using FlexPepDock
• peptide_specificity: Peptide Specificity
• peptide_specificity_using_FlexPepBind: Prediction of peptide binding using FlexPepBind

Noncanonicals

Utilities

• make_rot_lib: Making non-canonical amino acid rotamer libraries

Docking

• using_ncaas_protein_peptide_interface_design: Using NCAAs in Protein-Peptide Interface Design

Nucleic Acids

Structure Prediction

• DasLab_RNA_RosettaModelingTutorial: 3D RNA modeling
• mohca_seq: MOHCA-Seq: Modeling RNA with fragmentation data
• rna_puzzle: StepWise Monte Carlo (examples for RNA)
• rna_thread: RNA threading/mutation

Design

• rna_design: Fixed backbone design of RNA

Utilities

• nucleobase_sample_around: Nucleobase Sample Around
• rna_mutate: RNA mutation: Change RNA sequence

Loops

• stepwise_monte_carlo_rna_multiloop: Stepwise Monte Carlo RNA Multiloop
• swa_rna_loop: Application of the Stepwise Assembly method to RNA loop modeling (SWA_RNA_LOOP)

Interfaces

• protein_dna_interface_design: Protein DNA Interface Design
• protein_rna_interface_design: Protein-RNA Interface Design

Experimental Data

• auto-drrafter: auto-DRRAFTER: automatically build RNA coordinates into cryo-EM maps
• drrafter: DRRAFTER: De novo RNP modeling in Real-space through Assembly of Fragments Together with Experimental density in Rosetta
• erraser: ERRASER: Enumerative Real-Space Refinement ASsitted by Electron density under Rosetta

Rna

• farfar2: FARFAR2
• rna_denovo: RNA De Novo
• RNA_Denovo_with_base_pair_steps: Fragment assembly of RNA (FARNA) with base pair steps (-bps_moves).
• rnp_ddg: Calculate relative binding affinities for a RNA-protein complex

Rna

• recces: RECCES (Reweighting of Energy-function Collection with Conformational Ensemble Sampling)

Core Concepts

Docking

• numpy_kinematics: Rosetta-Style Kinematics in Numpy Syntax

Symmetry

• symmetry_examples: Symmetry Examples

Noncanonicals

• patched_residue_types_in_centroid-fullatom_protocols: Tutorial for using modified residue types in centroid-level applications.

General

• surface_docking_python: PyRosetta RosettaSurface

Other

• rosettanmr_readme: **Protocol capture to the manuscript "Integrative protein modeling in RosettaNMR from sparse paramagnetic restraints"**

Tcrmodel

Tcr

• tcr_modeling: TCRmodel Demo

Other

• test_keywords: Keyword Testing (Internal detail)

Protocol Captures

Many papers using Rosetta are accompanied by a protocol capture - an example of how to use the protocol discussed in the paper. The protocol captures below aren't meant to show the best way to solve problems in the current version of Rosetta, instead they are meant to show published solutions to problems that were addressed by members of the Rosetta community. The purpose of these protocol captures is both to serve as a historical record and to assist those trying to reproduce past results. See the demos (above) for updated versions of most protocol captures.

Full input files for the protocol captures are located in the demos/protocol_capture/ directory of the Rosetta distribution.

Structure Prediction

Utilities

• fragment_picking_for_cs_rosetta: Fragment Picking for CS-Rosetta
• fragment_picking_for_cs_talos_L1_rama: Fragment Picking for CS Talos L1 Rama

Experimental Data

• gps_rosetta_pcs_nmr_constraints: Capturing Conformational States in Proteins Using Pseudocontact Shifts (PCS)

Symmetry

• symmetry_examples: Symmetry Examples

General

• fragment_picking_with_psi_jufo_sam_L1_quota: Fragment Picking with Psi Jufo SAM L1 Quota
• fragment_picking_with_quota: Fragment Picking with Quota
• rhiju_four_small_puzzles: Four Small Puzzles
• stepwise_enumerative_assembly: Stepwise Enumerative Assembly

Design

Docking

• broker: Broker Protocol Captures

Peptides

• threefold_symmetric_peptide_design: Designing Threefold-Symmetric Meso-Sized Polypeptides With Threefold-Symmetric Cross-linkers

General

• backrub_seqtol: Backrub Sequence Tolerance
• peptide_designs: Peptide Backbone and Sequence Design
• ts_mutant: Temperature-Sensitive Mutation Prediciton

Utilities

General

• foldit_standalone: Foldit Standalone Protocol Capture
• rhiju_iron_chef_recipe: Rhiju Iron Chef Recipe

Scripting Interfaces

General

• rosetta_scripts: RosettaScripts

Loops

Structure Prediction

• next_generation_kic: Next Generation KIC

Membranes

• topology_broker_gpcr: Protocol Name:Loop Building for Membrane Proteins with Toplogy Broker

Docking

Interfaces

• canonical_sampling_docking: Canonical Sampling for Protein-Protein Docking Refinement
• replica_docking: Replica Docking

General

• gpcr_model_dock: GPCR Model Dock Protocol Capture

Interfaces

Design

• anchored_design: Anchored Design

Surfaces

General

• surface_docking_cpp: C++ RosettaSurface
• surface_docking_python: PyRosetta RosettaSurface

Experimental Data

Structure Prediction

• rasrec_evolutionary_restraints: RASREC Evolutionary Restraints

General

• spin_labels: Spin Labels

Membranes

Structure Prediction

• mp_mutate_relax: MP Mutate Relax Protocol Capture
• mp_relax: Membrane Relax
• original_mp_relax_menv_smooth: Membrane Relax with Menv_smooth Term

Analysis

• mp_score: MP Score Protocol Capture
• mp_transform_optimize: MP Transform Optimize Protocol Capture
• mp_visualize: MP Visualize Protocol Capture

Utilities

• mp_pymol_viewer: Visualizing Membranes in PyMOL
• mp_span_from_pdb: Spanfile from PDB

Docking

• mp_ddg: Membrane ΔΔG
• mp_dock: Membrane Protein-Protein Docking

Symmetry

• mp_symdock: Membrane Symmetric Protein-Protein Docking

Structure

• helix_from_sequence: Helix from sequence Protocol Capture

Antibodies

Design

• multistate_apl: Heterodimeric Antibody Design using Multistate Design

Ligands

Utilities

• rosettaligand_transform: RosettaLigand Transform

Docking

• ligand_water_docking: Ligand-centric Water Docking

Peptides

Structure Prediction

• flex_pep_dock_abinitio: FlexPepDock AbInitio Protocol Capture

Noncanonicals

Interfaces

• using_ncaas_protein_peptide_interface_design: Using NCAAs in Protein-Peptide Interface Design

Protein

Design

• loodo: LooDo (Loop-Directed Domain Insertion)

Under Development

If you want to prevent a demo from being published to the static wiki until you've finished developing it or written a paper on it or something, put it in demos/pilot. It will be visible here, but not on the public site.

Structure Prediction

Nucleic Acids

• rna_denovo_structure_pred: De novo structure prediction of small RNAs

General

• andrew: Running the fixbb protocol

General

General

• rna_design_rcon: This is the title of the demo