Computational Chemical and Structural Biology
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. 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.
|Topic||Tutorial text||Full Tutorial|
|Ab initio Folding||(87 MB)|
|Comparative Modeling||(33 MB)|
|Protein-Protein Docking||(32 MB)|
|Ligand Docking||(150 MB)|
|Protein Design||(31 MB)|
|Structure Refinement with Electron Density||(206 MB)|
|Topic||Tutorial text||Full Tutorial|
|Scoring and preparation||(2.5 MB)|
|Clustering with Calibur||(0.5 MB)|
17th Annual Great Lakes GPCR Conference (2016)A series of tutorials on comparative modeling and ligand docking were presented at this conference.
|Comparative Modeling & Ligand Docking (207 MB tar gzipped file)
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.
|Rosetta Membrane Workshop Files (730 MB zip file)
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.
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.
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
|Preparing and Scoring Structures with Rosetta
|Multi-template homology modeling with RosettaCM
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:
|Rosetta Energy Function
|Is this Model Good ?
|Preparing Your Structure
|Common File Formats in Rosetta
|Your Rosetta First Application
Rosetta Application Tutorials:
|Rosetta Ligand-Docking||N/A||Gordon Lemmon|
|Comparative Modeling, Loop Building and Clustering||Liz Dong|
|Protein-Protein Docking||Jordan Willis|
|Rosetta Enzyme Design
Additional Files from Workshop:
|Associated Scripts for Rosetta 3.2 Tutorials||
|Complete Rosetta Tutorial Files and Scripts (212 MB)**
† 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.