• Teaching Resources
  • Software
  • Movies
  • Rosetta Tutorials

Teaching Resources


Course Materials
Lecture Slides
Peer Review of Papers and Proposals
How to Prepare an Constructive, Fair, Unbiased, Effective Review

CHEM 337 - Computational Structural And Chemical Biology

Theoretical and practical aspects of protein sequence alignments,
secondary structure prediction, comparative modeling, protein-protein
and protein-ligand docking. Structure-based drug design, virtual
quantitative structure activity relations, cheminformatics, and
screening, pharmacophore mapping in therapeutic development.
This course includes a laboratory section.

Syllabus: pdf-download

Course Materials
Lecture Slides Materials for lab following lecture
To decompress myfile.tgz, type tar -xzvf myfile.tgz from a linux terminal
1: Course Overview and Introduction to Protein Structure pdf-download
2: Sequence-Sequence Alignment Methods pdf-download Intro to Linux: tar-download
3: Sequence Based Secondary Structure Prediction pdf-download
4: Protein Family Classification through Hidden Markov Models pdf-download Sequence-sequence alignment: tar-download
Secondary structure prediction: tar-download
Homework: tar-download
5: Fold Recognition & Sequence-Structure Alignment (Threading) pdf-download
6: Comparative Modelling and the Loop Closure Problem pdf-download Fold Recognition and Threading: tar-download
7: De-Novo Structure Prediction pdf-download
8: Modeling Protein Side Chains from Rotamer Libraries pdf-download Comparative Modelling/Loops: tar-download
9: Protein Structure Determination from Limited Experimental Datasets pdf-download
10: Protein Design pdf-download De Novo Structure Prediction: tar-download
10.5: Topic Overflow, Summary, First Exam Preparation Rotamer Library: tar-download
11: Structure-Structure Alignment Techniques and Fold Classification pdf-download tar-download
12: Protein-Protein Docking pdf-download
13: Protein-Ligand Docking pdf-download Docking: tar-download
14: Structure-based Virtual Screening & Drug Design pdf-download
15: Constitution, Configuration, & Conformation pdf-download Structure-Based Virtual Screening: tar-download
16: Structure Generators pdf-download Ligand-Based Virtual Screening: tar-download
17: Molecular Descriptors pdf-download
18: QSAR, Ligand-based Virtual Screening, and Pharmacophore Mapping pdf-download Pharmacophore Mapping: tar-download


Michael Müller, Kerstin Gräbe, Jens Meiler

Organochemical Pathways is a systematic review on typical reactions in organic chemistry on a poster and as a program running on windows 95/98/NT

Poster Screenshot
Image Image




Jens Meiler, 1999-2000
The program offers a fast and comfortable tool analyzing and handling dipolar coupling data. Powder pattern can be visualized, theoretical dipolar couplings can be calculated for a given structure and alignment and experimental values can be fitted over one or even a set of structures in order to perform e. g. a 3D homology search for proteins. A well distributed database extracted from the PDB is available. Moreover restraint files for XPlor and CNS calculations can be written. The program is written in Ansi C++ and the interface is Windows. All input and output files are given in Ascii format.

File dipocoup.zip
Help dipocoup_help.zip



Jens Meiler, 1998-1999

The program offers a fast and comfortable tool for creating, training and analyzing artificial back propagation neural networks on PC's. The program is written in Ansi C++ and the interface is Windows. All files containing the net and data information as well as all protocols are written in Ascii format.

File smart.zip


Introduction to Rosetta
Part 1 Part 2 Part 3
Part 1 Part 2 Part 3
Part 1 Part 2
Part 1 Part 2
Part 1 Part 2
Protein Folding (Ubiquitin) Protein Packing (TOP7) Protein Design (TOP7)
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 (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.



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.



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)





Older Workshop Materials


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


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
 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:


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)**


† 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.

Abinitio Folding
Protein Design
Protein Ligand Docking
Homology or Loop Modelling
Protein-Protein Docking
Additional Files from the Publication Supplement
Rosetta Tutorial: Input only
Rosetta Tutorial: Complete with Output Files