Table of Contents

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

Loops

Experimental Data

Peptides

Nucleic Acids

Denovo

General

Design

Utilities

Loops

Interfaces

Enzymes

Peptides

Noncanonicals

Metals

Stability Improvement

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

General

Analysis

Interfaces

General

Utilities

General

Scripting Interfaces

Design

Loops

Interfaces

Nucleic Acids

General

Loops

Design

Membranes

Nucleic Acids

General

Docking

Structure Prediction

Design

Analysis

Interfaces

Experimental Data

Symmetry

Ligands

Peptides

General

Interfaces

Design

General

Surfaces

Docking

Experimental Data

Structure Prediction

General

Membranes

Structure Prediction

Analysis

Utilities

Docking

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

Antibodies

Docking

Ligands

Structure Prediction

Utilities

Docking

Interfaces

Noncanonicals

Peptides

Design

Docking

Noncanonicals

Utilities

  • make_rot_lib: Making non-canonical amino acid rotamer libraries

Docking

Nucleic Acids

Structure Prediction

Design

Utilities

Loops

Interfaces

Experimental Data

  • erraser: ERRASER: Enumerative Real-Space Refinement ASsitted by Electron density under Rosetta

Rna

Rna

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

Core Concepts

Symmetry

Noncanonicals

General

Other

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

Experimental Data

Symmetry

General

Design

Docking

  • broker: Broker Protocol Captures

Peptides

General

Utilities

General

Scripting Interfaces

General

Loops

Structure Prediction

Membranes

Docking

Interfaces

General

Interfaces

Design

Surfaces

General

Experimental Data

Structure Prediction

General

Membranes

Structure Prediction

Analysis

Utilities

Docking

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

Symmetry

  • mp_symdock: Membrane Symmetric Protein-Protein Docking

Structure

Antibodies

Design

  • multistate_apl: Heterodimeric Antibody Design using Multistate Design

Ligands

Utilities

Docking

Peptides

Structure Prediction

Noncanonicals

Interfaces