Rosetta Tutorials

 

Image

 

Image

 

ROSETTA is a unified software package for protein structure prediction and functional design. It has been used to predict protein structures with and without the aid of sparse experimental data, perform protein-protein and protein-small molecule docking, design novel proteins and redesign existing proteins for altered function. ROSETTA allows for rapid tests of hypotheses in biomedical research which would be impossible or exorbitantly expensive to perform via traditional experimental methods.

 

Thereby, ROSETTA methods are becoming increasingly important in the interpretation of biological findings, e.g., from genome projects and in the engineering of therapeutics, probe molecules and model systems in biomedical research (Bender et al. "Protocols for Molecular Modeling with Rosetta3 and RosettaScripts." Biochemistry 2016. )

 








 

Complete tutorials for "Protocols for Molecular Modeling with Rosetta3 and RosettaScripts."

 

These are the complete tutorials (including all input files and example output files) for the protocols presented in Bender et al. "Protocols for Molecular Modeling with Rosetta3 and RosettaScripts." Biochemistry 2016. These tutorials are written to work with the Rosetta 3.6 release, using the updated talaris2014 energy function. Users of Rosetta 3.8 or later may need to use the Rosetta/tools/xsd_xrw/rewrite_rosetta_script.py script to convert the provided XMLs into the updated format. These tutorials contain step-by-step instructions for worked examples of the given protocol. A version of the tutorials with just the essential input files can be found as Supporting Information on the Biochemistry website.

 

 

Main Tutorials:

 

TopicTutorial textFull Tutorial
Ab initio Folding  pdf-download  zip-download (87 MB)
Comparative Modeling  pdf-download  zip-download (33 MB)
Protein-Protein Docking  pdf-download  zip-download (32 MB)
Ligand Docking  pdf-download  zip-download (150 MB)
Protein Design  pdf-download  zip-download (31 MB)
Structure Refinement with Electron Density  pdf-download  zip-download (206 MB)

 

Additional Materials:

 

TopicTutorial textFull Tutorial
Scoring and preparation  pdf-download  zip-download (2.5 MB)
Clustering with Calibur  pdf-download  zip-download (0.5 MB)

 

 


 

 

Special Topic Workshops

In addition to the generalized Rosetta Workshops, the Meiler lab regularly holds workshops which focus on the challenges particular to specific subfields.

 

 

Rosetta Antibody Workshop 2017

In conjunction with the BSDF conference at Vanderbilt, a workshop focusing on membrane proteins was held in April of 2017. Based on Rosetta 3.8, this workshop included hands-on tutorials for RosettaAntibody structure prediction, HCDR3 loop modeling, computational affinity maturation, antibody-antigen docking, epitope grafting onto scaffolds, and electron density refinement, as well as presentations on Rosetta basics.

 

 

Zip file (93 MB) of all presentations and tutorials for the 2017 workshop zip-download

 

TopicPresentationTutorialTutorial Materials
RosettaAntibody Structure Prediction
 pdf-download  pdf-download  zip-download
HCDR3 Loop Modeling
 pdf-download  pdf-download  zip-download
Design & Computational Affinity Maturation
 pdf-download  pdf-download  zip-download
Epitope Grafting
 pdf-download  pdf-download  zip-download
Antibody-Antigen Docking
 pdf-download  pdf-download  zip-download
Refinement into Electron Density
Tutorial by Dr. Frank Dimaio of the University of Washington

 

Short Talk TopicPresentation
Introduction to Antibodies
 pdf-download
Rosetta I/O
 pdf-download
Rosetta Energy Function
 pdf-download
RosettaScripts XML
 pdf-download
Using Experimental Data with Rosetta
 pdf-download

 

 

17th Annual Great Lakes GPCR Conference (2016)

A series of tutorials on comparative modeling and ligand docking were presented at this conference.
TopicTutorialsPresentation
Comparative Modeling & Ligand Docking (207 MB tar gzipped file)
 tar-download  pdf-download

 

 

Rosetta Membrane Workshop 2014

 

In conjunction with the BSDF conference at Vanderbilt, a workshop focusing on membrane proteins was held in April of 2014. Based on the Rosetta 2013wk52 weekly release, this workshop included hands-on tutorials for ab inito folding, homology modeling, protein-protein docking, ligand docking, and design of membrane proteins, as well as presentations on Rosetta basics and using Rosetta with membrane proteins. While examples focused on membrane proteins, these updated protocols can be adapted for use with soluble proteins as well.

 

TopicTutorials
Rosetta Membrane Workshop Files (730 MB zip file)
 zip-download


 

 


 

 

Older Workshop Materials

 

Materials from the November 2016 workshop

 

Below are the updated tutorials from the Rosetta Workshop held in November 2016 at Vanderbilt University. These tutorials are based on the Rosetta 3.7 release. These tutorials were covered during a 3-day hands-on workshop which included PowerPoint presentations and step-by-step instructions for worked examples.

 

  • zip-download Ab initio folding
  • zip-download RosettaCM multi-template comparative modeling
  • zip-download Protein-Protein docking
  • zip-download Protein-small molecule docking
  • zip-download Single and Multi-state protein design
  • zip-download Structural refinement with electron density
  • zip-download Short talks: Input and Output, Rosetta Energy Function, RosettaScripts, Using experimental data

 

Materials from the November 2015 workshop

 

Below are the updated tutorials from the Rosetta Workshop held in November 2015 at Vanderbilt University. These tutorials are based on the Rosetta 2015.31 weekly release. These tutorials were covered during a 3-day hands-on workshop which included PowerPoint presentations and step-by-step instructions for worked examples.

 

Main Tutorials

 

  • zip-download Ab initio folding
  • zip-download RosettaCM multi-template comparative modeling
  • zip-download Protein-Protein docking
  • zip-download Protein-small molecule docking
  • zip-download Protein design
  • zip-download Structural refinement with electron density
  • zip-download Short talks: IO, Model evaluation, RosettaScripts, Rosetta Energy Function, Using experimental data

 

Additional Materials

 

  • zip-download Preparing and Scoring Structures with Rosetta
  • zip-download New RosettaMP membrane framework. (Scoring, relax, docking, and ddG)
  • zip-download Single template comparative modeling (includes Rosetta clustering tutorial).
  • zip-download Additional material (includes Glossary, vHTS, MPI, Calibur clustering, Linux, and visualization.)

 

 

Tutorials from December 2014

 

For a class at Leipzig University in December 2014, two new tutorials were prepared. These tutorials are a supplement to the other tutorials, and are based on the 2014wk35 weekly release

 

TopicTutorials
Preparing and Scoring Structures with Rosetta
 zip-download
Multi-template homology modeling with RosettaCM
 zip-download

 

 

Updated Tutorials from Rosetta Workshop 2011

 

Below are the updated tutorials from the Rosetta Workshop, held in March 2011 at Vanderbilt University. These tutorials are based on the Rosetta 3.2.1 release version. These tutorials were covered during a 2-day hands-on workshop which included PowerPoint presentations of each topic and step-by-step instructions on working examples for ab initio folding, comparative modeling, loop building, clustering, ligand docking and protein docking. :

 

Introduction to Rosetta:


TopicPresentationMoviesPresenter
Rosetta Energy Function
 pdf-download icon Steven Combs
Is this Model Good ?
 pdf-download Steven Combs
Preparing Your Structure
 pdf-download Steven Combs
Common File Formats in Rosetta
 pdf-download Steven Combs
Your Rosetta First Application
 pdf-download Steven Combs

 

Rosetta Application Tutorials:

 

TopicPresentationTutorialsMoviesPresenter
Folding  pdf-download  pdf-download icon Stephanie Hirst
Rosetta Ligand-Docking  N/A  pdf-download icon Gordon Lemmon
Comparative Modeling, Loop Building and Clustering  pdf-download  pdf-download icon Liz Dong
Protein-Protein Docking   pdf-download  pdf-download icon Jordan Willis
Rosetta Enzyme Design
 N/A pdf-download  N/A Steven Combs

 

Additional Files from Workshop:


Associated Scripts for Rosetta 3.2 Tutorials  tar-download

Sam Deluca

Complete Rosetta Tutorial Files and Scripts (212 MB)**
 tar-download

 

† Exception: clean_pdb.py done by Phil Bradley, Rhiju Das, Michael Tyka, TJ Brunette, James Thompson, Steven Combs

* tar archive for all the Tutorials pdf

** tar archive for Tutorials and Scripts

 

Original Rosetta Workshop 2010 Files

 

The following are the Rosetta Tutorials originally published with "Practically Useful: What the Rosetta Protein Modeling Suite Can Do for You", Kaufman et. al. Biochemistry 2010. These tutorials are based on the Rosetta 3.0 release version and include tutorials on ab initio folding, clustering, design, ligand docking, loop modeling, protein docking and refinement.



TopicTutorials
Abinitio Folding
 pdf-download
Clustering
 pdf-download
Protein Design
 pdf-download
Protein Ligand Docking
 pdf-download
Homology or Loop Modelling
 pdf-download
Protein-Protein Docking
 pdf-download
Refinement/Relaxtion
 pdf-download
Additional Files from the Publication Supplement
Rosetta Tutorial: Input only
 zip-download
Rosetta Tutorial: Complete with Output Files
 zip-download