September 30, 2015
||St Johns Innovation Centre|
Cowley Road, Cambridge, CB4 0WS, UK
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Introduction to Biologics Modeling
The course covers analysis of an antibody structure, starting from the sequence of an antibody, using the antibody homology modeler. The surface of the model is analyzed with the Surfaces and Maps application, and the Protein Patch Analyzer. Protein properties are predicted, including titration over a range of pH values. The model is then compared with an X-ray structure of the antibody in complex with its antigen which shows that the features identified from the model make key interactions with the antigen. Next the structure of a human antibody is compared with structures from similar antibodies to identify regions with structural conservation, and with human germline sequences to show the positions of somatic mutations in the structure.
Peptide Therapeutics and Peptidomimetic Design
The course covers structure-based approaches for peptide design. More specifically, the interaction of a cocrystallized peptide-protein complex will be evaluated by generating and examining the molecular surface topology and visualizing protein contacts in 3D. The effect of sequence mutations are explored to both natural and non-natural amino acids. This uses an interactive editor and the Protein Design application for scanning on specific residues in the context of peptide affinity optimization. A protocol for adding a non-natural amino acid to the residue rotamer library is also described.
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