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Current Opinion in Structural Biology
Article . 2025 . Peer-reviewed
License: CC BY
Data sources: Crossref
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Prediction of structural variation

Authors: Yogesh Kalakoti; Airy Sanjeev; Björn Wallner;

Prediction of structural variation

Abstract

Proteins are dynamic molecules that transition between conformational states to perform their functions, and characterizing the protein ensemble is important for understanding biology and therapeutic applications. While recent breakthroughs in machine learning have enabled the prediction of high-quality static models of individual proteins, generating reliable estimates of their conformational ensembles remains a challenge. Several recent methods have tried to utilize the evolutionary and structural features captured by effective sequence-to-structure models to enhance conformational diversity in generated models. Most of these approaches involve adapting existing inference pipelines, such as AlphaFold 2, combined with sampling techniques to induce the generation of diverse conformational states. Here, we describe the general problem of predicting structural variations in protein systems, explain the methods designed to address this challenge, explore why they are effective, discuss their limitations, and suggest potential future directions.

Country
Sweden
Related Organizations
Keywords

Models, Molecular, Machine Learning, Protein Conformation, Biophysics, Proteins, Computational Biology, Biochemistry, Biokemi, Biofysik

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citations
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
3
Average
Average
Average
Green
hybrid