Building Solid Foundations for a Structure Based Design Campaign – Workshop handout Erice 2008

Simon Bowden, Peter Carlqvist, John Liebeschuetz

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Part 1 Validation of Structural Models and Comparative Binding-Site Analysis

A. Analysing a protein structure for errors and interesting features

B. Comparing a structure with structures related by homology or by functionality

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Part 2 Analysing Protein-Ligand Interactions

A. Substructure searching in Relibase

B. Comparing the interactions of different ligands with the same target

C. Validating an unusual interaction using substructure searching in Relibase