Meiler Lab Computational Chemical and Structural Biology |
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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. To teach a wider audience how to effectively use Rosetta, the Meiler lab holds a regular hands-on workshop. Materials from these workshops can be found below, or in several publications. (Bender et al. "Protocols for Molecular Modeling with Rosetta3 and RosettaScripts." Biochemistry 2016 and Kaufman et al. "Practically Useful: What the Rosetta Protein Modeling Suite Can Do for You" Biochemistry 2010 )
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:
Additional Materials:
Topic | Tutorial text | Full Tutorial |
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Scoring and preparation | (2.5 MB) | |
Clustering with Calibur | (0.5 MB) |
Materials from the November 2018 workshop
Below are the updated tutorials from the Rosetta Workshop held in November 2018 at Vanderbilt University.
These tutorials have been updated to work with the recent REF2015 energy function, and are based on the Rosetta 2018.42.60459 weekly release. They should also mostly work with the Rosetta 3.10 release, though the 3.10 release has a bug in the InterfaceAnalyzer mover used in some of the tutorials.
These tutorials were covered during a 3-day hands-on workshop which included PowerPoint presentations and step-by-step instructions for worked examples.
Rosetta Antibody Tutorials 2020
Files | Topic |
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Rosetta Antibody | |
Rosetta Antibody-2 | |
Rosetta Antibody-3 | |
Rosetta Antibody-4 | |
Scaffolding | |
Protein Docking | |
rabd Design | |
Glycan Modeling | |
hcdr3 Modeling | |
Affinity Maturation |
Rosetta Antibody Workshop 2019
A workshop focusing on antibodies was held in April of 2019. Based on Rosetta weekly release 2019.07, this workshop included hands-on tutorials for RosettaAntibody structure prediction, antibody-antigen docking, computational affinity maturation, antibody structure redesign, glycan modeling, and epitope grafting onto scaffolds, as well as presentations on Rosetta basics.
Short Talk Topic | Presentation |
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Introduction to Antibodies | |
Navigating Rosetta and I/O | |
RosettaScripts XML | |
Rosetta Energy Function |
Rosetta Protein Design Workshop 2018
A workshop focusing on membrane proteins was held in May of 2018. Based on Rosetta 3.9, this workshop included hands-on tutorials for structure prediction of modified proteins, thermostabilization, single and multistate design, small molecule interface design, peptide design, scaffold and motif grafting as well as presentations on Rosetta basics.
17th Annual Great Lakes GPCR Conference (2016)
A series of tutorials on comparative modeling and ligand docking were presented at this conference.Topic | Tutorials | Presentation |
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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.
Topic | Tutorials |
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Rosetta Membrane Workshop Files (730 MB zip file) |
Materials from the December 2017 workshop
Below are the updated tutorials from the Rosetta Workshop held in December 2017 at Vanderbilt University.
These tutorials have been updated to work with the recent REF2015 energy function, and are based on the Rosetta 2017.36.59679 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.
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.
Topic | Presentation | Tutorial | Tutorial Materials |
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RosettaAntibody Structure Prediction |
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HCDR3 Loop Modeling |
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Design & Computational Affinity Maturation |
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Epitope Grafting |
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Antibody-Antigen Docking |
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Refinement into Electron Density |
Tutorial by Dr. Frank Dimaio of the University of Washington |
Short Talk Topic | Presentation |
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Introduction to Antibodies | |
Rosetta I/O |
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Rosetta Energy Function |
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RosettaScripts XML |
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Using Experimental Data with Rosetta |
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.
Main Tutorials
Additional Materials
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
Topic | Tutorials |
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Preparing and Scoring Structures with Rosetta |
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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 Application Tutorials:
Additional Files from Workshop:
Associated Scripts for Rosetta 3.2 Tutorials |
Sam Deluca† |
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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.