Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

ATLIGATOR: Editing protein interactions with an atlas-based approach

Josef Paul Kynast, Felix Schwägerl, View ORCID ProfileBirte Höcker
doi: https://doi.org/10.1101/2022.01.19.476980
Josef Paul Kynast
1Department for Biochemistry, University of Bayreuth, Bayreuth, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Felix Schwägerl
1Department for Biochemistry, University of Bayreuth, Bayreuth, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Birte Höcker
1Department for Biochemistry, University of Bayreuth, Bayreuth, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Birte Höcker
  • For correspondence: birte.hoecker@uni-bayreuth.de
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Data/Code
  • Preview PDF
Loading

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.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/Hoecker-Lab/atligator

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
Back to top
PreviousNext
Posted January 21, 2022.
Download PDF
Data/Code
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
ATLIGATOR: Editing protein interactions with an atlas-based approach
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
ATLIGATOR: Editing protein interactions with an atlas-based approach
Josef Paul Kynast, Felix Schwägerl, Birte Höcker
bioRxiv 2022.01.19.476980; doi: https://doi.org/10.1101/2022.01.19.476980
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
ATLIGATOR: Editing protein interactions with an atlas-based approach
Josef Paul Kynast, Felix Schwägerl, Birte Höcker
bioRxiv 2022.01.19.476980; doi: https://doi.org/10.1101/2022.01.19.476980

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Bioinformatics
Subject Areas
All Articles
  • Animal Behavior and Cognition (3589)
  • Biochemistry (7553)
  • Bioengineering (5498)
  • Bioinformatics (20742)
  • Biophysics (10305)
  • Cancer Biology (7962)
  • Cell Biology (11624)
  • Clinical Trials (138)
  • Developmental Biology (6596)
  • Ecology (10175)
  • Epidemiology (2065)
  • Evolutionary Biology (13586)
  • Genetics (9525)
  • Genomics (12824)
  • Immunology (7911)
  • Microbiology (19518)
  • Molecular Biology (7647)
  • Neuroscience (42014)
  • Paleontology (307)
  • Pathology (1254)
  • Pharmacology and Toxicology (2195)
  • Physiology (3260)
  • Plant Biology (7027)
  • Scientific Communication and Education (1294)
  • Synthetic Biology (1948)
  • Systems Biology (5420)
  • Zoology (1113)