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Updated: Oct 26, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Characterizing the fragmentation of AlphaFold predictions
Frédéric Cazals1, Edoardo Sarti1
1Algorithms-Biology-Structure, Centre Inria d'Université Côte d'Azur, 06902 Sophia-Antipolis, France.
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.
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