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

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

SUBMITTER: Verwimp S 

PROVIDER: S-EPMC12619643 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature