Suche nach Personen

plus im Publikationsserver
plus bei Google Scholar

Bibliografische Daten exportieren
 

PocketOptimizer 2.0 : A modular framework for computer‐aided ligand‐binding design

DOI zum Zitieren der Version auf EPub Bayreuth: https://doi.org/10.15495/EPub_UBT_00007093
URN zum Zitieren der Version auf EPub Bayreuth: urn:nbn:de:bvb:703-epub-7093-8

Titelangaben

Noske, Jakob ; Kynast, Josef ; Lemm, Dominik ; Schmidt, Steffen ; Höcker, Birte:
PocketOptimizer 2.0 : A modular framework for computer‐aided ligand‐binding design.
In: Protein Science. Bd. 32 (2023) Heft 1 . - No. e4516.
ISSN 1469-896X
DOI der Verlagsversion: https://doi.org/10.1002/pro.4516

Volltext

[thumbnail of Protein Science - 2022 - Noske - PocketOptimizer 2 0 A modular framework for computer‐aided ligand‐binding design.pdf]
Format: PDF
Name: Protein Science - 2022 - Noske - PocketOptimizer 2 0 A modular framework for computer‐aided ligand‐binding design.pdf
Version: Veröffentlichte Version
Verfügbar mit der Lizenz Creative Commons BY 4.0: Namensnennung
Download (1MB)

Abstract

The ability to design customized proteins to perform specific tasks is of great interest. We are particularly interested in the design of sensitive and specific small molecule ligand-binding proteins for biotechnological or biomedical applications. Computational methods can narrow down the immense combinatorial space to find the best solution, and thus provide starting points for experimental procedures. However, success rates strongly depend on accurate modelling and energetic evaluation. Not only intra- but also intermolecular interactions have to be considered. To address this problem, we developed PocketOptimizer, a modular computational protein design pipeline, that predicts mutations in the binding pockets of proteins to increase affinity for a specific ligand. Its modularity enables users to compare different combinations of force fields, rotamer libraries, and scoring functions. Here we present a much-improved version - PocketOptimizer 2.0. We implemented a cleaner user interface, an extended architecture with more supported tools such as force fields and scoring functions, a backbone-dependent rotamer library, as well as different improvements in the underlying algorithms. Version 2.0 was tested against a benchmark of design cases and assessed in comparison to the first version. Our results show how the newly implemented features such as the new rotamer library can lead to improved prediction accuracy. Therefore, we believe that PocketOptimizer 2.0 with its many new and improved functionalities provides a robust and versatile environment for the design of small molecule binding pockets in proteins. It is widely applicable and extendible due to its modular framework. PocketOptimizer 2.0 can be downloaded at https://github.com/Hoecker-Lab/pocketoptimizer. This article is protected by copyright. All rights reserved.

Weitere Angaben

Publikationsform: Artikel in einer Zeitschrift
Themengebiete aus DDC: 500 Naturwissenschaften und Mathematik
500 Naturwissenschaften und Mathematik > 500 Naturwissenschaften
500 Naturwissenschaften und Mathematik > 540 Chemie
500 Naturwissenschaften und Mathematik > 570 Biowissenschaften; Biologie
Institutionen der Universität: Fakultäten
Fakultäten > Fakultät für Biologie, Chemie und Geowissenschaften
Fakultäten > Fakultät für Biologie, Chemie und Geowissenschaften > Fachgruppe Chemie
Fakultäten > Fakultät für Biologie, Chemie und Geowissenschaften > Fachgruppe Chemie > Lehrstuhl Biochemie I - Proteinbiochemie der Signaltransduktion
Fakultäten > Fakultät für Biologie, Chemie und Geowissenschaften > Fachgruppe Chemie > Lehrstuhl Biochemie III - Proteindesign > Lehrstuhl Biochemie III - Proteindesign - Univ.-Prof. Dr. Birte Höcker
Fakultäten > Fakultät für Biologie, Chemie und Geowissenschaften > Fachgruppe Chemie > Professur Biochemie
Fakultäten > Fakultät für Biologie, Chemie und Geowissenschaften > Fachgruppe Chemie > Lehrstuhl Biochemie III - Proteindesign
Sprache: Englisch
Titel an der UBT entstanden: Ja
URN: urn:nbn:de:bvb:703-epub-7093-8
Eingestellt am: 14 Jul 2023 07:07
Letzte Änderung: 14 Jul 2023 07:07
URI: https://epub.uni-bayreuth.de/id/eprint/7093

Downloads

Downloads pro Monat im letzten Jahr