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Updated: Jul 4, 2025

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Sequence clustering confounds AlphaFold2.

Joseph W Schafer¹, Devlina Chakravarty¹, Ethan A Chen¹

¹National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894.

Biorxiv : the Preprint Server for Biology

|February 5, 2024

Summary

This summary is machine-generated.

AF-cluster struggles to predict metamorphic protein structures, often mistaking single-folded proteins for fold-switchers. Random sequence sampling with ColabFold offers a more reliable and efficient alternative for predicting protein structures.

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Area of Science:

Protein structure prediction
Computational biology
Biophysics

Background:

Globular proteins can switch between multiple conformations, termed metamorphic proteins.
AlphaFold2 (AF2) accurately predicts dominant protein structures but often fails to capture alternative conformations.
Predicting these alternative structures is crucial for understanding protein function and regulation.

Conclusions:

AF-cluster is an unreliable predictor of metamorphic protein structures due to methodological flaws.
The method misclassifies single-folding proteins and exhibits poor confidence calibration.
ColabFold-based random sequence sampling, potentially augmented with other methods, is recommended as a more accurate and computationally efficient alternative.