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Teaching Resources

RESPONSIBLE CONDUCT IN RESEARCH


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



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



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



Poster Screenshot
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Software

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


 

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
Miscellaneous
Protein Folding (Ubiquitin) Protein Packing (TOP7) Protein Design (TOP7)
Rosetta Tutorials

 

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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 (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.

 

 

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

 

 

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:


TopicPresentationMoviesPresenter
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:

 

TopicPresentationTutorialsMoviesPresenter
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)**
 tar-download

 

† 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