Rosetta Tutorials

 

 

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:

 

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)

 

Additional Materials:

 

Topic	Tutorial text	Full Tutorial
Scoring and preparation		(2.5 MB)
Clustering with Calibur		(0.5 MB)

 

 

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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.

 

 

Files	Topic
	Ab initio folding
	RosettaCM multi-template comparative modeling
	Protein-Protein docking
	Protein-small molecule docking
	Single and Multi-state protein design
	Scaffolding and sidechain/backbone (epitope) grafting
	Short talks: Input and Output, Navigating Rosetta, Rosetta Energy Function, RosettaScripts, Using experimental data

 

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 Tutorials 2020

Files	Topic
	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.

Topic	Presentation	Tutorial	Tutorial Materials
RosettaAntibody Structure Prediction
Antibody-Antigen Docking
Computational Affinity Maturation
RosettaAntibodyDesign (with Jared Adolf-Bryfogle)
Glycan Modeling (with Jared Adolf-Bryfogle)
Epitope Grafting

 

Short Talk Topic	Presentation
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.

Topic	Presentation	Tutorial	Tutorial Materials
RosettaCM Prediction of Designed Structures
Thermostabilization and General Protein Design
Antibody Single & Multistate Design
Enzyme and protein-small molecule interface design
Peptide Design
Protein Scaffold and Motif Design

 

Short Talk Topic	Presentation
Rosetta Basics: IO and Navigating Rosetta
Creating Custom Protocols with RosettaScripts
Rosetta Scoring (or Energy) Function
Structure preparation
High Throughput Experiments and Rosetta Design

 

 

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
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
Rosetta Membrane Workshop Files (730 MB zip file)

 

 

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Older Workshop Materials

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.

 

 

Files	Topic
	Ab initio folding
	RosettaCM multi-template comparative modeling
	Protein-Protein docking
	Protein-small molecule docking
	Single and Multi-state protein design
	Scaffolding and sidechain/backbone (epitope) grafting
	Short talks: Input and Output, Navigating Rosetta, Rosetta Energy Function, RosettaScripts, Using experimental data

 

 

 

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

 

Short Talk Topic	Presentation
Introduction to Antibodies
Rosetta I/O
Rosetta Energy Function
RosettaScripts XML
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.

 

• Ab initio folding
• RosettaCM multi-template comparative modeling
• Protein-Protein docking
• Protein-small molecule docking
• Single and Multi-state protein design
• Structural refinement with electron density
• 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

 

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

 

Additional Materials

 

• Preparing and Scoring Structures with Rosetta
• New RosettaMP membrane framework. (Scoring, relax, docking, and ddG)
• Single template comparative modeling (includes Rosetta clustering tutorial).
• 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

 

Topic	Tutorials
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:

Topic	Presentation	Movies	Presenter
Rosetta Energy Function			Steven Combs
Is this Model Good ?			Steven Combs
Preparing Your Structure			Steven Combs
Common File Formats in Rosetta			Steven Combs
Your Rosetta First Application			Steven Combs

 

Rosetta Application Tutorials:

 

Topic	Presentation	Tutorials	Movies	Presenter
Folding				Stephanie Hirst
Rosetta Ligand-Docking	N/A			Gordon Lemmon
Comparative Modeling, Loop Building and Clustering				Liz Dong
Protein-Protein Docking				Jordan Willis
Rosetta Enzyme Design	N/A		N/A	Steven Combs

 

Additional Files from Workshop:

Associated Scripts for Rosetta 3.2 Tutorials		Sam Deluca†
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