PocketOptimizer and the Design of Ligand Binding Sites.
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.
Max Planck Institute for Developmental Biology, Tübingen, Germany.
Andre C
AC
Stiel
Max Planck Institute for Developmental Biology, Tübingen, Germany.
Mehdi
M
Nellen
Max Planck Institute for Developmental Biology, Tübingen, Germany. birte.hoecker@uni-bayreuth.de.|Lehrstuhl für Biochemie, Universität Bayreuth, Bayreuth, Germany. birte.hoecker@uni-bayreuth.de.
Birte
B
Höcker
D001665:Binding Sites; D008024:Ligands; D011506:Proteins / Q000737:chemistry*
D008024:Ligands; D011506:Proteins
Computational protein design; Enzyme engineering; Ligand binding design; PocketOptimizer; Protein–small molecule interaction