February 12, 2015
||Centre for Bioinformatics at the University of Hamburg|
Bundesstrasse 45, 20146, Hamburg, Germany
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Inhibitor Design Using MOE SBDD Applications
This hands-on course covers the application of in silico structure based drug design (SBDD) tools for the rational design of Tarceva-based EGFR kinase inhibitors. Starting with raw PDB protein-ligand 3D structures, all the steps required to initiate and advance an SBDD study are covered: preparing PDB structures for modelling, binding pocket visualization, protein-ligand contact analysis and the use of SAR for in situ modelling (modifying and optimizing ligands in the binding pocket) to design new compounds. Advanced topics such as pharmacophore query generation, protein-ligand docking, protein alignments for binding site comparison and in situ combinatorial synthesis will also be covered.
Analyzing and Optimizing Protein-Protein Interactions
The course covers tools in MOE for analyzing protein-protein interactions, such as molecular surfaces and non-bonded contact visualization in 3D and using 2D interaction diagrams. Examples include calculating surface properties such as electrostatic hot-spots or patches, as well as physicochemical properties such as the isoelectric focusing point and zeta potential. The effect of mutations on protein-protein interactions generated through the protein engineering applications will also be explored.
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