AFragmenter: schema-free, tuneable protein domain segmentation for AlphaFold protein structures

Bioinformatics, vol. 41

Abstract

SUMMARY: Protein domain segmentation is a crucial aspect of understanding protein functions and interactions, and it is vital for protein modelling exercises and evolutionary studies. Current segmentation methods often rely on predefined classification schemes, leading to inconsistencies and biases. AFragmenter provides a schema-free and tuneable approach to protein domain segmentation based on network analysis of AlphaFold-predicted structures. Utilizing Predicted Aligned Error values, AFragmenter constructs a fully connected network of protein residues and identifies distinct structural domains by using Leiden clustering. This method empowers users to adjust parameters including contrast threshold and resolution, providing control over the segmentation process. AVAILABILITY AND IMPLEMENTATION: AFragmenter is implemented in Python3 and freely available under an MIT license. It can be found as a Python library and command line tool at https://github.com/sverwimp/AFragmenter, pip, and Conda.

Authors 4

1. Stefaan Verwimp

   KU Leuven

   Affiliation as printed

   Department of Biosystems, KU Leuven , Leuven 3001,

   Department of Microbial and Molecular Systems, KU Leuven , Leuven 3001,

   Department of Biosystems, KU Leuven, Leuven, 3001, Belgium

   Molecular Systems Department of Microbial and , KU 3001, Belgium Leuven, Leuven

2. Rob Lavigne

   KU Leuven

   Affiliation as printed

   Department of Biosystems, KU Leuven , Leuven 3001,

   Department of Biosystems, KU Leuven, Leuven, 3001, Belgium

3. Cédric Lood corresponding

   University of Oxford

   Affiliation as printed

   Department of Biology, University of Oxford , Oxford OX1 3SZ,

   Department of Biology, University of Oxford, Oxford, OX1 3SZ, United Kingdom

4. Vera van Noort corresponding Aachen Institute of Biology Leiden

   Leiden University · KU Leuven

   Affiliation as printed

   Department of Microbial and Molecular Systems, KU Leuven , Leuven 3001,

   Institute of Biology Leiden, Leiden University , Leiden 2333 BE,

   Institute of Biology Leiden, Leiden University, Leiden, 2333 BE, The Netherlands

   Molecular Systems Department of Microbial and , KU 3001, Belgium Leuven, Leuven