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PocketOptimizer and the Design of Ligand Binding Sites

Title data

Stiel, André C. ; Nellen, Mehdi ; Höcker, Birte:
PocketOptimizer and the Design of Ligand Binding Sites.
In: Stoddard, Barry L. (ed.): Computational Design of Ligand Binding Proteins. - New York : Humana Press , 2016 . - pp. 63-75 . - (Methods in Molecular Biology ; 1414 ) (Springer protocols)
ISBN 978-1-4939-3569-7
DOI: https://doi.org/10.1007/978-1-4939-3569-7_5

Abstract in another language

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.

Further data

Item Type: Article in a book
Refereed: Yes
Institutions of the University: Faculties > Faculty of Biology, Chemistry and Earth Sciences
Faculties > Faculty of Biology, Chemistry and Earth Sciences > Department of Chemistry
Faculties > Faculty of Biology, Chemistry and Earth Sciences > Department of Chemistry > Chair Biochemistry
Faculties > Faculty of Biology, Chemistry and Earth Sciences > Department of Chemistry > Chair Biochemistry > Chair Biochemistry - Univ.-Prof. Dr. Birte Höcker
Faculties
Result of work at the UBT: No
DDC Subjects: 500 Science
500 Science > 540 Chemistry
Date Deposited: 02 Jun 2017 05:52
Last Modified: 02 Jun 2017 05:52
URI: https://eref.uni-bayreuth.de/id/eprint/37237