PocketOptimizer and the Design of Ligand Binding Sites

Stiel, AC; Nellen, M; Höcker, B

doi:10.1007/978-1-4939-3569-7_5

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PocketOptimizer and the Design of Ligand Binding Sites

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Stiel, AC
Research Group Protein Design, Max Planck Institute for Developmental Biology, Max Planck Society;

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Nellen, M
Research Group Protein Design, Max Planck Institute for Developmental Biology, Max Planck Society;

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Höcker, B
Research Group Protein Design, Max Planck Institute for Developmental Biology, Max Planck Society;

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Citation

Stiel, A., Nellen, M., & Höcker, B. (2016). PocketOptimizer and the Design of Ligand Binding Sites. In Methods in Molecular Biology. US: Springer.

Cite as: https://hdl.handle.net/21.11116/0000-000A-7C4E-5

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.