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PocketOptimizer and the Design of Ligand Binding Sites
Andre C Stiel1, Mehdi Nellen1, Birte Höcker2,3
1Max Planck Institute for Developmental Biology, Tübingen, Germany.
Abstract:
PocketOptimizer is a computational method to design protein binding pockets that has been recently developed. Starting from a protein structure an existing small molecule binding pocket is optimized for the recognition of a new ligand. The modular program predicts mutations that will improve the affinity of a target small molecule to the protein of interest using a receptor-ligand scoring function to estimate the binding free energy. PocketOptimizer has been tested in a comprehensive benchmark and predicted mutations have also been used in experimental tests. In this chapter, we will provide general recommendations for usage as well as an in-depth description of all individual PocketOptimizer modules.
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