RESPONSIBLE CONDUCT IN RESEARCH

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:

ORGANOCHEMICAL PATHWAYS

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

File: pathways.zip

Poster Screenshot

DIPOCOUP

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

SMART

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

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 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 (Kaufmann, K. W.; Lemmon, G. H.; Deluca, S. L.; Sheehan, J. H.; Meiler, J. "Practically Useful: What the Rosetta Protein Modeling Suite Can Do for You" Biochemistry 2010.)

 

Rosetta Tutorials originally published with "Practically Useful: What the Rosetta Protein Modeling Suite Can Do for You" Biochemistry 2010" are below. 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.

 

 

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

 

 

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