Work

Characterizing the fragmentation of AlphaFold predictions

Year: 2026

Type: article

Abstract: Motivation The Nobel Prize-winning program AlphaFold2 computes plausible structures of (well) folded proteins. The main quality assessment is based on the predicted local distance difference test (pLDDT), a per-amino acid confidence score. Results To enhance quality assessment, we provide novel quantitative measures to identify coherent amino acid (a.a.) stretches along the sequence in terms of pLDDT values. These constructions, grounded in standard techniques from topological data analysis and combinatorics, provide a canonical framework for identifying regions along the protein backbone and analyzing their properties, such as their propensity for disorder and their consistency with a null model. The outcome of our analysis can readily be used to select reliable regions/domains within proteins whose pLDDT values span the entire pLDDT range. Results Availability and implementation: The software acompanying this work is available in the package Alphafold_analysis of the Structural Bioinformatics Library.

Source: Bioinformatics Advances

DOI: 10.1093/bioadv/vbag186

Authors: Frédéric Cazals, Edoardo Sarti

Institutions: Université Côte d'Azur, Centre Inria d'Université Côte d'Azur

Language: English

Topic: Protein Structure and Dynamics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $2,726

Funder: Agence Nationale de la Recherche