Demos Grouped by Keyword

Structure Prediction

• abinitio: AbInitio: Predict structure from sequence
• 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
• AbPredict: AbPredict
• analyzing_interface_quality: Analyzing Interface Quality
• anchored_design: Anchored Design
• andrew: Running the fixbb protocol
• auto-drrafter: auto-DRRAFTER: automatically build RNA coordinates into cryo-EM maps
• backrub_seqtol: Backrub Sequence Tolerance
• beta_strand_homodimer_design: β-Strand Homodimer Design
• broker_ubq: Topology Broker - AbInitio with a given beta strand topology
• canonical_sampling_docking: Canonical Sampling for Protein-Protein Docking Refinement
• comparative_modeling: Comparative Modeling: Single template modeling and loop building
• confchangemover_membrane: ConfChangeMover for membrane proteins
• confchangemover_soluble: ConfChangeMover for soluble proteins
• cryo_em_tutorial: Modeling using low to medium resolution cryoEM data.
• cs_rosetta_rna: CS-Rosetta RNA: Using chemical shifts with RNA structure refinement
• DasLab_RNA_RosettaModelingTutorial: 3D RNA modeling
• Denovo_structure_prediction: *De novo* structure prediction
• design_with_phosphoresidue: Design with Phosphoresidues
• drrafter: DRRAFTER: De novo RNP modeling in Real-space through Assembly of Fragments Together with Experimental density in Rosetta
• farfar2: FARFAR2
• fixbb: Demo for the fixbb application
• flex_pep_dock_abinitio: FlexPepDock AbInitio Protocol Capture
• floppy_tail: Floppy Tail Demo
• folding_tutorial: Protein Folding using the Broker
• fragment_picking: Standard fragment picking
• fragment_picking_for_cs_rosetta: Fragment Picking for CS-Rosetta
• fragment_picking_for_cs_rosetta: Fragment Picking for CS-Rosetta
• fragment_picking_for_cs_talos_L1_rama: Fragment Picking for CS Talos L1 Rama
• fragment_picking_with_psi_jufo_sam_L1_quota: Fragment Picking with Psi Jufo SAM L1 Quota
• fragment_picking_with_quota: Fragment Picking with Quota
• gpcr_model_dock: GPCR Model Dock Protocol Capture
• gps_rosetta_pcs_nmr_constraints: Capturing Conformational States in Proteins Using Pseudocontact Shifts (PCS)
• gps_rosetta_pcs_nmr_constraints: Capturing Conformational States in Proteins Using Pseudocontact Shifts (PCS)
• homology_modeling_threading_basic: Basic Homology Modeling Demo
• hrf_rosetta: Rescoring Rosetta Models using low resolution HRF Mass Spectrometry Data
• membrane_abinitio: Membrane ab initio modeling
• membrane_folding_tutorial: Membrane Protein Folding
• membrane_homology_modeling: Membrane Homology Modeling
• model_missing_loop: Model a Missing Loop
• mohca_seq: MOHCA-Seq: Modeling RNA with fragmentation data
• molecular_replacement: Molecular Replacement Demo
• mp_mutate_relax: MP Mutate Relax Protocol Capture
• mp_relax: Membrane Relax
• mp_relax: Membrane Relax
• next_generation_kic: Next Generation KIC
• Optimizing_Sidechains_The_Packer: Optimizing Side-Chains: Introduction to the *Packer*
• original_mp_relax_menv_smooth: Membrane Relax with Menv_smooth Term
• original_mp_relax_menv_smooth: Membrane Relax with Menv_smooth Term
• Protein-Protein-Docking: Protein-Protein Docking
• rasrec_evolutionary_restraints: RASREC Evolutionary Restraints
• refinement_of_protein_peptide_complex_using_FlexPepDock: Refinement of peptide-protein complexes using FlexPepDock refinement
• Relax: Relax
• relax_a_large_structure: Relax a Large Structure
• relax_around_chemically_bound_ligand: Relax Around A Chemically Bound Ligand
• rhiju_four_small_puzzles: Four Small Puzzles
• rna_assembly: RNA Assembly
• rna_denovo: RNA De Novo
• rna_denovo_structure_pred: De novo structure prediction of small RNAs
• RNA_Denovo_with_base_pair_steps: Fragment assembly of RNA (FARNA) with base pair steps (-bps_moves).
• rna_puzzle: StepWise Monte Carlo (examples for RNA)
• rna_thread: RNA threading/mutation
• rnp_structure_prediction: Structure prediction of an RNA-protein complex
• rosetta_cm_tutorial: Comparative Modeling: Multi-template modeling with RosettaCM
• rosettaligand_transform: RosettaLigand Transform
• spin_labels: Spin Labels
• stepwise_enumerative_assembly: Stepwise Enumerative Assembly
• stepwise_enumerative_assembly: Stepwise Enumerative Assembly
• stepwise_monte_carlo_mini_protein: StepWise Monte Carlo to build a small protein
• stepwise_monte_carlo_protein_loop: StepWise Monte Carlo (example for protein loop)
• stepwise_monte_carlo_rna_multiloop: Stepwise Monte Carlo RNA Multiloop
• structure_refinement: Rosetta tools for structure determination in density
• swa_protein_main: SWA Protein Main
• symmetry_examples: Symmetry Examples
• symmetry_examples: Symmetry Examples
• xl_driven_protein_docking: Crosslink Guided Protein-Protein Docking

Design

• anchored_design: Anchored Design
• anchored_design: Anchored Design
• backrub_seqtol: Backrub Sequence Tolerance
• beta_peptide_modeling: Beta-3-peptide design
• beta_strand_homodimer_design: β-Strand Homodimer Design
• broker: Broker Protocol Captures
• broker_domain_insertion: Toplogy Broker - Domain Insertion Protocol Capture
• Constraints: Constraints Tutorial
• design_raf_rac_interface: Design the Rac/Raf interface
• design_with_flex_loops: Design with flexible loops
• design_with_ncaa: Design with non-canonical amino acids (NCAA)
• domain_insertion: Domain Insertion Demo
• doug_dock_design_min: Doug's DockDesignMinimize Demo
• enzyme_design: Enzyme Design Demo
• favor_native_residue: Favor Native Residue
• fixbb_design: Demo for the fixbb application with design
• ideal_proteins: Design of Proteins with Ideal Topologies
• loodo: LooDo (Loop-Directed Domain Insertion)
• multi_state_desing_of_antibodies: Multistate Design of Antibodies
• multistate_apl: Heterodimeric Antibody Design using Multistate Design
• next_generation_kic: Next Generation KIC
• oop_design: Oop Design: Design with oligooxopiperazine helix mimetics
• Optimizing_Sidechains_The_Packer: Optimizing Side-Chains: Introduction to the *Packer*
• peptide_designs: Peptide Backbone and Sequence Design
• peptide_designs: Peptide Backbone and Sequence Design
• protein_design_tutorial: Protein Design
• rna_design: Fixed backbone design of RNA
• rosetta_scripts_enzdes: Rosetta scripts: enzdes
• rosetta_scripts_flxbb_design: Flexible backbone design with RosettaScripts
• rosetta_scripts_pp-interfaceredesign: Protein protein interface design using rosetta scripts
• rosetta_scripts_RosettaDNA: Rosetta scripts: Rosetta-DNA Demo
• shortening_loops: Shortening loops in Rosetta
• stepwise_monte_carlo_rna_loop: StepWise Monte Carlo of an RNA loop
• supercharge: Supercharge: Reengineer proteins for high net surface charge
• symmetry_examples: Symmetry Examples
• threefold_symmetric_peptide_design: Designing Threefold-Symmetric Meso-Sized Polypeptides With Threefold-Symmetric Cross-linkers
• threefold_symmetric_peptide_design: Designing Threefold-Symmetric Meso-Sized Polypeptides With Threefold-Symmetric Cross-linkers
• ts_mutant: Temperature-Sensitive Mutation Prediciton
• ts_mutant: Temperature-Sensitive Mutation Prediciton
• vip: Rosetta VIP: Void Indentification and Packing
• zinc_site_redesign: Zinc Site Redesign

Analysis

• Analysis: Analysis Tutorial: Interpreting Rosetta Outputs
• analyzing_interface_quality: Analyzing Interface Quality
• calculate_protein_protein_ddg: Calculate Protein Protein ΔΔG
• clustering: Clustering: Group similar decoys with the Rosetta cluster application.
• fullatom_centroid: Full Atom Representation vs Centroid Representation
• mp_pymol_viewer: Visualizing Membranes in PyMOL
• mp_score: MP Score Protocol Capture
• mp_span_from_pdb: Spanfile from PDB
• mp_transform_optimize: MP Transform Optimize Protocol Capture
• mp_visualize: MP Visualize Protocol Capture
• predict_eglinC_ddgs: Predict DDGs for the eglinC protein
• scoring: Scoring Tutorial
• scoring_and_prep: PDB scoring and preparation with Rosetta
• ts_mutant: Temperature-Sensitive Mutation Prediciton
• unfolded_state_energy_calculator: Instructions for Calculating Explicit Unfolded State Energies for Noncanonical Amino Acids

Utilities

• favor_native_residue: Favor Native Residue
• foldit_standalone: Foldit Standalone Protocol Capture
• foldit_standalone: Foldit Standalone Protocol Capture
• fragment_picking: Standard fragment picking
• fragment_picking_for_cs_rosetta: Fragment Picking for CS-Rosetta
• fragment_picking_for_cs_rosetta: Fragment Picking for CS-Rosetta
• fragment_picking_for_cs_talos_L1_rama: Fragment Picking for CS Talos L1 Rama
• input_and_output: Controlling Input and Output in Rosetta
• make_rot_lib: Making non-canonical amino acid rotamer libraries
• mp_pymol_viewer: Visualizing Membranes in PyMOL
• mp_pymol_viewer: Visualizing Membranes in PyMOL
• mp_span_from_pdb: Spanfile from PDB
• nucleobase_sample_around: Nucleobase Sample Around
• optE: optE: Refit Rosetta reference energies
• optimize_ligand_hydroxyl_hydrogens: Optimize Ligand Hydroxyl Hydrogens
• prepare_pdb_for_rosetta_with_relax: Relax with all-heavy-atom constraints
• prepare_pdbs_for_rosetta: Prepare PDBs for Rosetta
• rhiju_iron_chef_recipe: Rhiju Iron Chef Recipe
• rna_mutate: RNA mutation: Change RNA sequence
• rosettaligand_transform: RosettaLigand Transform
• scoring: Scoring Tutorial
• scoring_and_prep: PDB scoring and preparation with Rosetta

Scripting Interfaces

• advanced_scripting_with_rosettascripts: More Advanced RosettaScripts Concepts
• generalized_kinematic_closure_1: Generalized Kinematic Closure Tutorial 1:
• generalized_kinematic_closure_2: Generalized Kinematic Closure Tutorial 2:
• generalized_kinematic_closure_3: Generalized Kinematic Closure Tutorial 3:
• generalized_kinematic_closure_4: Generalized Kinematic Closure Tutorial 4:
• rosetta_scripts: RosettaScripts
• rosetta_scripts: RosettaScripts example scripts
• rosetta_scripts_enzdes: Rosetta scripts: enzdes
• rosetta_scripts_flxbb_design: Flexible backbone design with RosettaScripts
• rosetta_scripts_LoopRemodel: Loop Remodel
• rosetta_scripts_pp-interfaceredesign: Protein protein interface design using rosetta scripts
• rosetta_scripts_RosettaDNA: Rosetta scripts: Rosetta-DNA Demo
• scripting_with_rosettascripts: Creating protocols with RosettaScripts

Loops

• comparative_modeling: Comparative Modeling: Single template modeling and loop building
• design_with_flex_loops: Design with flexible loops
• generalized_kinematic_closure_1: Generalized Kinematic Closure Tutorial 1:
• generalized_kinematic_closure_2: Generalized Kinematic Closure Tutorial 2:
• generalized_kinematic_closure_3: Generalized Kinematic Closure Tutorial 3:
• generalized_kinematic_closure_4: Generalized Kinematic Closure Tutorial 4:
• loop_modeling: Loop Modeling
• model_missing_loop: Model a Missing Loop
• next_generation_kic: Next Generation KIC
• next_generation_kic: Next Generation KIC
• rosetta_scripts_LoopRemodel: Loop Remodel
• shortening_loops: Shortening loops in Rosetta
• stepwise_monte_carlo_protein_loop: StepWise Monte Carlo (example for protein loop)
• stepwise_monte_carlo_rna_loop: StepWise Monte Carlo of an RNA loop
• stepwise_monte_carlo_rna_multiloop: Stepwise Monte Carlo RNA Multiloop
• swa_protein_long_loop: SWA Protein Loop Long
• swa_protein_main: SWA Protein Main
• swa_rna_loop: Application of the Stepwise Assembly method to RNA loop modeling (SWA_RNA_LOOP)
• topology_broker_gpcr: Protocol Name:Loop Building for Membrane Proteins with Toplogy Broker
• topology_broker_gpcr: Protocol Name:Loop Building for Membrane Proteins with Toplogy Broker

Docking

• abinitio_fold_and_dock_of_peptides_using_flexpepdock: AbInitio fold-and-dock of peptides using FlexPepDock
• advanced_protein-protein_docking_tutorial: Protein-Protein Docking
• antibody_docking: Antibody Docking
• broker: Broker Protocol Captures
• broker_snugdock: Toplogy Broker - SnugDock Protocol Capture
• canonical_sampling_docking: Canonical Sampling for Protein-Protein Docking Refinement
• canonical_sampling_docking: Canonical Sampling for Protein-Protein Docking Refinement
• chemically_conjugated_docking: Chemically Conjugated Docking
• darc: DARC Demo
• dock_protein_complex_with_ligand_xml: Dock protein complex with ligand
• dock_with_user_defined_constraints: Docking with constraints
• doug_dock_design_min: Doug's DockDesignMinimize Demo
• flex_pep_dock_abinitio: FlexPepDock AbInitio Protocol Capture
• gpcr_model_dock: GPCR Model Dock Protocol Capture
• gpcr_model_dock: GPCR Model Dock Protocol Capture
• hbs_design: HBS Design Demo
• ligand_dock_commandline: Ligand Dock Demo
• ligand_docking_tutorial: Ligand Docking
• ligand_water_docking: Ligand-centric Water Docking
• ligand_water_docking: Ligand-centric Water Docking
• mp_ddg: Membrane ΔΔG
• mp_ddg: Membrane ΔΔG
• mp_dock: Membrane Protein-Protein Docking
• mp_dock: Membrane Protein-Protein Docking
• mp_symdock: Membrane Symmetric Protein-Protein Docking
• numpy_kinematics: Rosetta-Style Kinematics in Numpy Syntax
• peptide_specificity: Peptide Specificity
• peptide_specificity_using_FlexPepBind: Prediction of peptide binding using FlexPepBind
• predict_eglinC_ddgs: Predict DDGs for the eglinC protein
• Protein-Protein-Docking: Protein-Protein Docking
• refinement_of_protein_peptide_complex_using_FlexPepDock: Refinement of peptide-protein complexes using FlexPepDock refinement
• replica_docking: Replica Docking
• replica_docking: Replica Docking
• surface_docking_cpp: C++ RosettaSurface
• symmetric_docking_insulin_trimer_of_dimers: Symmetric Docking of Insulin Trimer of Dimers - Demo
• symmetry_examples: Symmetry Examples
• using_ncaas_protein_peptide_interface_design: Using NCAAs in Protein-Peptide Interface Design
• xl_driven_protein_docking: Crosslink Guided Protein-Protein Docking

Interfaces

• advanced_protein-protein_docking_tutorial: Protein-Protein Docking
• analyzing_interface_quality: Analyzing Interface Quality
• anchored_design: Anchored Design
• anchored_design: Anchored Design
• beta_strand_homodimer_design: β-Strand Homodimer Design
• calculate_protein_protein_ddg: Calculate Protein Protein ΔΔG
• canonical_sampling_docking: Canonical Sampling for Protein-Protein Docking Refinement
• design_raf_rac_interface: Design the Rac/Raf interface
• dock_protein_complex_with_ligand_xml: Dock protein complex with ligand
• dock_with_user_defined_constraints: Docking with constraints
• interface_design_demo: Interface Design Demo
• peptide_designs: Peptide Backbone and Sequence Design
• peptide_specificity_using_FlexPepBind: Prediction of peptide binding using FlexPepBind
• protein_dna_interface_design: Protein DNA Interface Design
• protein_rna_interface_design: Protein-RNA Interface Design
• refinement_of_protein_peptide_complex_using_FlexPepDock: Refinement of peptide-protein complexes using FlexPepDock refinement
• relax_around_chemically_bound_ligand: Relax Around A Chemically Bound Ligand
• replica_docking: Replica Docking
• replica_docking: Replica Docking
• rnp_ddg: Calculate relative binding affinities for a RNA-protein complex
• rnp_structure_prediction: Structure prediction of an RNA-protein complex
• rosetta_scripts_pp-interfaceredesign: Protein protein interface design using rosetta scripts
• rosetta_scripts_RosettaDNA: Rosetta scripts: Rosetta-DNA Demo
• using_ncaas_protein_peptide_interface_design: Using NCAAs in Protein-Peptide Interface Design
• using_ncaas_protein_peptide_interface_design: Using NCAAs in Protein-Peptide Interface Design
• zinc_site_redesign: Zinc Site Redesign

Surfaces

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

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
• auto-drrafter: auto-DRRAFTER: automatically build RNA coordinates into cryo-EM maps
• cryo_em_tutorial: Modeling using low to medium resolution cryoEM data.
• 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
• gps_rosetta_pcs_nmr_constraints: Capturing Conformational States in Proteins Using Pseudocontact Shifts (PCS)
• hrf_rosetta: Rescoring Rosetta Models using low resolution HRF Mass Spectrometry Data
• molecular_replacement: Molecular Replacement Demo
• rasrec_evolutionary_restraints: RASREC Evolutionary Restraints
• rasrec_evolutionary_restraints: RASREC Evolutionary Restraints
• spin_labels: Spin Labels
• spin_labels: Spin Labels
• structure_refinement: Rosetta tools for structure determination in density
• xl_driven_protein_docking: Crosslink Guided Protein-Protein Docking

Symmetry

• mp_symdock: Membrane Symmetric Protein-Protein Docking
• protein_design_tutorial: Protein Design
• symmetric_docking_insulin_trimer_of_dimers: Symmetric Docking of Insulin Trimer of Dimers - Demo
• Symmetry: Symmetry Tutorial
• symmetry_examples: Symmetry Examples
• symmetry_examples: Symmetry Examples

Membranes

• helix_from_sequence: Helix from sequence Protocol Capture
• membrane_abinitio: Membrane ab initio modeling
• membrane_folding_tutorial: Membrane Protein Folding
• membrane_homology_modeling: Membrane Homology Modeling
• mp_ddg: Membrane ΔΔG
• mp_ddg: Membrane ΔΔG
• mp_dock: Membrane Protein-Protein Docking
• mp_dock: Membrane Protein-Protein Docking
• mp_mutate_relax: MP Mutate Relax Protocol Capture
• mp_pymol_viewer: Visualizing Membranes in PyMOL
• mp_pymol_viewer: Visualizing Membranes in PyMOL
• mp_relax: Membrane Relax
• mp_relax: Membrane Relax
• mp_score: MP Score Protocol Capture
• mp_span_from_pdb: Spanfile from PDB
• mp_span_from_pdb: Spanfile from PDB
• mp_symdock: Membrane Symmetric Protein-Protein Docking
• mp_symdock: Membrane Symmetric Protein-Protein Docking
• mp_transform_optimize: MP Transform Optimize Protocol Capture
• mp_visualize: MP Visualize Protocol Capture
• original_mp_relax_menv_smooth: Membrane Relax with Menv_smooth Term
• original_mp_relax_menv_smooth: Membrane Relax with Menv_smooth Term
• protein_design_tutorial: Protein Design
• topology_broker_gpcr: Protocol Name:Loop Building for Membrane Proteins with Toplogy Broker
• topology_broker_gpcr: Protocol Name:Loop Building for Membrane Proteins with Toplogy Broker

Antibodies

• AbPredict: AbPredict
• antibody_docking: Antibody Docking
• broker_snugdock: Toplogy Broker - SnugDock Protocol Capture
• multistate_apl: Heterodimeric Antibody Design using Multistate Design

Enzymes

• enzyme_design: Enzyme Design Demo
• rosetta_scripts_enzdes: Rosetta scripts: enzdes
• zinc_site_redesign: Zinc Site Redesign

Ligands

• chemically_conjugated_docking: Chemically Conjugated Docking
• darc: DARC Demo
• design_with_phosphoresidue: Design with Phosphoresidues
• dock_protein_complex_with_ligand_xml: Dock protein complex with ligand
• hbs_design: HBS Design Demo
• ligand_dock_commandline: Ligand Dock Demo
• ligand_docking_tutorial: Ligand Docking
• ligand_water_docking: Ligand-centric Water Docking
• ligand_water_docking: Ligand-centric Water Docking
• optimize_ligand_hydroxyl_hydrogens: Optimize Ligand Hydroxyl Hydrogens
• prepare_ligand_tutorial: Preparing Ligands
• relax_around_chemically_bound_ligand: Relax Around A Chemically Bound Ligand
• rosettaligand_transform: RosettaLigand Transform
• rosettaligand_transform: RosettaLigand Transform

Peptides

• abinitio_fold_and_dock_of_peptides_using_flexpepdock: AbInitio fold-and-dock of peptides using FlexPepDock
• beta_peptide_modeling: Beta-3-peptide design
• flex_pep_dock_abinitio: FlexPepDock AbInitio Protocol Capture
• flex_pep_dock_abinitio: FlexPepDock AbInitio Protocol Capture
• oop_design: Oop Design: Design with oligooxopiperazine helix mimetics
• peptide_specificity: Peptide Specificity
• peptide_specificity_using_FlexPepBind: Prediction of peptide binding using FlexPepBind
• refinement_of_protein_peptide_complex_using_FlexPepDock: Refinement of peptide-protein complexes using FlexPepDock refinement
• threefold_symmetric_peptide_design: Designing Threefold-Symmetric Meso-Sized Polypeptides With Threefold-Symmetric Cross-linkers
• threefold_symmetric_peptide_design: Designing Threefold-Symmetric Meso-Sized Polypeptides With Threefold-Symmetric Cross-linkers
• using_ncaas_protein_peptide_interface_design: Using NCAAs in Protein-Peptide Interface Design

Noncanonicals

• design_with_ncaa: Design with non-canonical amino acids (NCAA)
• design_with_phosphoresidue: Design with Phosphoresidues
• make_rot_lib: Making non-canonical amino acid rotamer libraries
• patched_residue_types_in_centroid-fullatom_protocols: Tutorial for using modified residue types in centroid-level applications.
• using_ncaas_protein_peptide_interface_design: Using NCAAs in Protein-Peptide Interface Design
• using_ncaas_protein_peptide_interface_design: Using NCAAs in Protein-Peptide Interface Design

Metals

• zinc_site_redesign: Zinc Site Redesign

Nucleic Acids

• auto-drrafter: auto-DRRAFTER: automatically build RNA coordinates into cryo-EM maps
• cs_rosetta_rna: CS-Rosetta RNA: Using chemical shifts with RNA structure refinement
• DasLab_RNA_RosettaModelingTutorial: 3D RNA modeling
• 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
• farfar2: FARFAR2
• mohca_seq: MOHCA-Seq: Modeling RNA with fragmentation data
• nucleobase_sample_around: Nucleobase Sample Around
• protein_dna_interface_design: Protein DNA Interface Design
• protein_rna_interface_design: Protein-RNA Interface Design
• rna_assembly: RNA Assembly
• rna_denovo: RNA De Novo
• rna_denovo_structure_pred: De novo structure prediction of small RNAs
• RNA_Denovo_with_base_pair_steps: Fragment assembly of RNA (FARNA) with base pair steps (-bps_moves).
• rna_design: Fixed backbone design of RNA
• rna_mutate: RNA mutation: Change RNA sequence
• rna_puzzle: StepWise Monte Carlo (examples for RNA)
• rna_thread: RNA threading/mutation
• rnp_ddg: Calculate relative binding affinities for a RNA-protein complex
• rnp_structure_prediction: Structure prediction of an RNA-protein complex
• rosetta_scripts_RosettaDNA: Rosetta scripts: Rosetta-DNA Demo
• stepwise_monte_carlo_rna_loop: StepWise Monte Carlo of an RNA loop
• 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)

Dna

• protein_dna_interface_design: Protein DNA Interface Design
• rosetta_scripts_RosettaDNA: Rosetta scripts: Rosetta-DNA Demo

Rna

• auto-drrafter: auto-DRRAFTER: automatically build RNA coordinates into cryo-EM maps
• cs_rosetta_rna: CS-Rosetta RNA: Using chemical shifts with RNA structure refinement
• DasLab_RNA_RosettaModelingTutorial: 3D RNA modeling
• 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
• farfar2: FARFAR2
• protein_rna_interface_design: Protein-RNA Interface Design
• recces: RECCES (Reweighting of Energy-function Collection with Conformational Ensemble Sampling)
• rna_assembly: RNA Assembly
• rna_denovo: RNA De Novo
• rna_denovo_structure_pred: De novo structure prediction of small RNAs
• RNA_Denovo_with_base_pair_steps: Fragment assembly of RNA (FARNA) with base pair steps (-bps_moves).
• rna_design: Fixed backbone design of RNA
• rna_mutate: RNA mutation: Change RNA sequence
• rna_puzzle: StepWise Monte Carlo (examples for RNA)
• rna_thread: RNA threading/mutation
• rnp_ddg: Calculate relative binding affinities for a RNA-protein complex
• rnp_structure_prediction: Structure prediction of an RNA-protein complex
• stepwise_monte_carlo_rna_loop: StepWise Monte Carlo of an RNA loop
• 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)

Denovo

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

Stability Improvement

• mp_mutate_relax: MP Mutate Relax Protocol Capture
• ts_mutant: Temperature-Sensitive Mutation Prediciton
• vip: Rosetta VIP: Void Indentification and Packing

Comparative Modeling

• rosetta_cm_tutorial: Comparative Modeling: Multi-template modeling with RosettaCM
• symmetry_examples: Symmetry Examples

Core Concepts

• advanced_scripting_with_rosettascripts: More Advanced RosettaScripts Concepts
• commonly_used_options: Commonly used options (generic options)
• Core_Concepts: Core Rosetta Concepts
• fold_tree: Fold tree
• fullatom_centroid: Full Atom Representation vs Centroid Representation
• input_and_output: Controlling Input and Output in Rosetta
• install_build: Installing Rosetta
• minimization: Finding Local Energy Minima Using the *Minimizer*
• numpy_kinematics: Rosetta-Style Kinematics in Numpy Syntax
• Optimizing_Sidechains_The_Packer: Optimizing Side-Chains: Introduction to the *Packer*
• patched_residue_types_in_centroid-fullatom_protocols: Tutorial for using modified residue types in centroid-level applications.
• prepare_ligand_tutorial: Preparing Ligands
• scoring: Scoring Tutorial
• scripting_with_rosettascripts: Creating protocols with RosettaScripts
• surface_docking_python: PyRosetta RosettaSurface
• symmetry_examples: Symmetry Examples
• Tips: Tips for using Rosetta
• Tutorial_Setup: How To Read These Tutorials
• working_with_rosetta: Working With Rosetta

General

• abinitio: AbInitio: Predict structure from sequence
• Analysis: Analysis Tutorial: Interpreting Rosetta Outputs
• andrew: Running the fixbb protocol
• backrub_seqtol: Backrub Sequence Tolerance
• backrub_seqtol: Backrub Sequence Tolerance
• broker_domain_insertion: Toplogy Broker - Domain Insertion Protocol Capture
• broker_snugdock: Toplogy Broker - SnugDock Protocol Capture
• broker_ubq: Topology Broker - AbInitio with a given beta strand topology
• clustering: Clustering: Group similar decoys with the Rosetta cluster application.
• commonly_used_options: Commonly used options (generic options)
• confchangemover_membrane: ConfChangeMover for membrane proteins
• confchangemover_soluble: ConfChangeMover for soluble proteins
• Constraints: Constraints Tutorial
• Core_Concepts: Core Rosetta Concepts
• Denovo_structure_prediction: *De novo* structure prediction
• domain_insertion: Domain Insertion Demo
• fixbb: Demo for the fixbb application
• fixbb_design: Demo for the fixbb application with design
• floppy_tail: Floppy Tail Demo
• fold_tree: Fold tree
• folding_tutorial: Protein Folding using the Broker
• foldit_standalone: Foldit Standalone Protocol Capture
• foldit_standalone: Foldit Standalone Protocol Capture
• fragment_picking_with_psi_jufo_sam_L1_quota: Fragment Picking with Psi Jufo SAM L1 Quota
• fragment_picking_with_quota: Fragment Picking with Quota
• gpcr_model_dock: GPCR Model Dock Protocol Capture
• gps_rosetta_pcs_nmr_constraints: Capturing Conformational States in Proteins Using Pseudocontact Shifts (PCS)
• homology_modeling_threading_basic: Basic Homology Modeling Demo
• ideal_proteins: Design of Proteins with Ideal Topologies
• input_and_output: Controlling Input and Output in Rosetta
• install_build: Installing Rosetta
• interface_design_demo: Interface Design Demo
• loop_modeling: Loop Modeling
• minimization: Finding Local Energy Minima Using the *Minimizer*
• multi_state_desing_of_antibodies: Multistate Design of Antibodies
• optE: optE: Refit Rosetta reference energies
• Optimizing_Sidechains_The_Packer: Optimizing Side-Chains: Introduction to the *Packer*
• peptide_designs: Peptide Backbone and Sequence Design
• prepare_pdb_for_rosetta_with_relax: Relax with all-heavy-atom constraints
• prepare_pdbs_for_rosetta: Prepare PDBs for Rosetta
• Protein-Protein-Docking: Protein-Protein Docking
• protein_design_tutorial: Protein Design
• rasrec_evolutionary_restraints: RASREC Evolutionary Restraints
• Relax: Relax
• relax_a_large_structure: Relax a Large Structure
• rhiju_four_small_puzzles: Four Small Puzzles
• rhiju_iron_chef_recipe: Rhiju Iron Chef Recipe
• rna_design_rcon: This is the title of the demo
• rosetta_scripts: RosettaScripts
• rosetta_scripts: RosettaScripts example scripts
• scoring: Scoring Tutorial
• spin_labels: Spin Labels
• stepwise_enumerative_assembly: Stepwise Enumerative Assembly
• stepwise_enumerative_assembly: Stepwise Enumerative Assembly
• supercharge: Supercharge: Reengineer proteins for high net surface charge
• surface_docking_cpp: C++ RosettaSurface
• surface_docking_python: PyRosetta RosettaSurface
• surface_docking_python: PyRosetta RosettaSurface
• swa_protein_long_loop: SWA Protein Loop Long
• Symmetry: Symmetry Tutorial
• Tips: Tips for using Rosetta
• ts_mutant: Temperature-Sensitive Mutation Prediciton
• Tutorial_Setup: How To Read These Tutorials
• unfolded_state_energy_calculator: Instructions for Calculating Explicit Unfolded State Energies for Noncanonical Amino Acids
• working_with_rosetta: Working With Rosetta