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Structural and Chemical Biology @ Vanderbilt University |
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Teaching Resources
After an introduction into the field; sequence databases, and sequence alignment tools will be briefly introduced. The importance of these tools to understand the evolution of proteins will be illustrated. The course will cover secondary structure prediction of proteins as well as prediction of other property related alphabets from the primary structure. Related methods such as artificial neural networks (ANN), support vector machines (SVM), and hidden Markov models (HMM) will be discussed.
The protein tertiary structure prediction section of the course will discuss homology modeling, fold recognition techniques, loop modeling, as well as de novo structure prediction. An introduction to various potential functions and energy minimization techniques will be given. The Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiment will be discussed.
A set of lectures will cover the field of protein design. The most important methods in this field will be introduced addressing the challenge of optimizing sequence as well as structural space at the same time. Applications for the computational design of new folds, protein-protein interactions, as well as enzymes will be discussed.
Methods for the computational analysis of protein-protein interactions will be introduced in the next section including docking calculations and interface analysis. This discussion will be enhanced onto protein-DNA interactions and protein-ligand interactions. The application of such tools in virtual drug screening and development will be shown.
Lecture Slides
Tutorials
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
Software
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.
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.
Servers
You can find all the servers here.
Movies
Simulating Protein Folding, Packing, and Design with ROSETTA:
Teaching Resources
CHEM 238 - Computational Structural Biochemistry
After an introduction into the field; sequence databases, and sequence alignment tools will be briefly introduced. The importance of these tools to understand the evolution of proteins will be illustrated. The course will cover secondary structure prediction of proteins as well as prediction of other property related alphabets from the primary structure. Related methods such as artificial neural networks (ANN), support vector machines (SVM), and hidden Markov models (HMM) will be discussed.
The protein tertiary structure prediction section of the course will discuss homology modeling, fold recognition techniques, loop modeling, as well as de novo structure prediction. An introduction to various potential functions and energy minimization techniques will be given. The Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiment will be discussed.
A set of lectures will cover the field of protein design. The most important methods in this field will be introduced addressing the challenge of optimizing sequence as well as structural space at the same time. Applications for the computational design of new folds, protein-protein interactions, as well as enzymes will be discussed.
Methods for the computational analysis of protein-protein interactions will be introduced in the next section including docking calculations and interface analysis. This discussion will be enhanced onto protein-DNA interactions and protein-ligand interactions. The application of such tools in virtual drug screening and development will be shown.
Lecture Slides
Tutorials
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
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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 |
Servers
SERVERS
You can find all the servers here.
Movies
Simulating Protein Folding, Packing, and Design with ROSETTA:
| Name | MPEG | size | WMV | size |
| Protein Folding (Ubiquitin)[1,2,3]: | 1ubi.mpeg | 10MB | 1ubi.wmv | 4MB |
| Protein Packing (TOP7)[4]: | top7_repack.mpeg | 8MB | top7_repack.wmv | 2MB |
| Protein Design (TOP7) [4]: | top7_design.mpeg | 16MB | top7_design.wmv | 5MB |
[2] R. Bonneau, C. E. M. Strauss, C. Rohl, D. Chivian, P. Bradley, L. Malmström, T. Robertson, D. Baker, De Novo Prediction of Three-dimensional Structures for Major Protein Families, J. Mol. Biol. 2002, 322, 65-78.
[4] B. Kuhlman, G. Dantas, G. C. Ireton, G. Varani, B. L. Stoddard, D. Baker, Design of a Novel Globular Protein Fold with Atomic Level Accuracy, Science 2003, 302, 1364-1368.