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ATLIGATOR : editing protein interactions with an atlas-based approach

Titelangaben

Kynast, Josef ; Schwägerl, Felix ; Höcker, Birte:
ATLIGATOR : editing protein interactions with an atlas-based approach.
In: Bioinformatics. Bd. 38 (2022) Heft 23 . - S. 5199-5205.
ISSN 1367-4803
DOI: https://doi.org/10.1093/bioinformatics/btac685

Abstract

Motivation: Recognition of specific molecules by proteins is a fundamental cellular mechanism and relevant for many applications. Being able to modify binding is a key interest and can be achieved by repurposing established interaction motifs. We were specifically interested in a methodology for the design of peptide binding modules. By leveraging interaction data from known protein structures, we plan to accelerate the design of novel protein or peptide binders.

Results: We developed ATLIGATOR-a computational method to support the analysis and design of a protein's interaction with a single side chain. Our program enables the building of interaction atlases based on structures from the PDB. From these atlases pocket definitions are extracted that can be searched for frequent interactions. These searches can reveal similarities in unrelated proteins as we show here for one example. Such frequent interactions can then be grafted onto a new protein scaffold as a starting point of the design process. The ATLIGATOR tool is made accessible through a python API as well as a CLI with python scripts.

Availability and implementation: Source code can be downloaded at github (https://www.github.com/Hoecker-Lab/atligator), installed from PyPI ('atligator') and is implemented in Python 3.

Weitere Angaben

Publikationsform: Artikel in einer Zeitschrift
Begutachteter Beitrag: Ja
Institutionen der Universität: 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
Fakultäten > Fakultät für Biologie, Chemie und Geowissenschaften > Fachgruppe Chemie > Lehrstuhl Biochemie > Lehrstuhl Biochemie III - Proteindesign - Univ.-Prof. Dr. Birte Höcker
Fakultäten > Fakultät für Biologie, Chemie und Geowissenschaften > Fachgruppe Chemie > Professur Biochemie
Fakultäten
Titel an der UBT entstanden: Ja
Themengebiete aus DDC: 500 Naturwissenschaften und Mathematik > 500 Naturwissenschaften
500 Naturwissenschaften und Mathematik > 540 Chemie
500 Naturwissenschaften und Mathematik > 570 Biowissenschaften; Biologie
Eingestellt am: 09 Dec 2022 06:20
Letzte Änderung: 09 Dec 2022 09:42
URI: https://eref.uni-bayreuth.de/id/eprint/72979