at Google ScholarTitle data
Kynast, Josef ; Schwägerl, Felix ; Höcker, Birte:
ATLIGATOR : editing protein interactions with an atlas-based approach.
In: Bioinformatics.
Vol. 38
(2022)
Issue 23
.
- pp. 5199-5205.
ISSN 1367-4803
DOI: https://doi.org/10.1093/bioinformatics/btac685
Abstract in another language
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.
Further data
| Item Type: | Article in a journal |
|---|---|
| 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 > Faculty of Biology, Chemistry and Earth Sciences > Department of Chemistry > Professorship Biochemistry Faculties |
| Result of work at the UBT: | Yes |
| DDC Subjects: | 500 Science > 500 Natural sciences 500 Science > 540 Chemistry 500 Science > 570 Life sciences, biology |
| Date Deposited: | 09 Dec 2022 06:20 |
| Last Modified: | 09 Dec 2022 09:42 |
| URI: | https://eref.uni-bayreuth.de/id/eprint/72979 |