ArticleMethods in enzymology2023
Combining small angle X-ray scattering (SAXS) with protein structure predictions to characterize conformations in solution.
Article in Methods in enzymology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- Hidden structural states of proteins revealed by conformer selection.Nature communications · 2026Article
- Experimental Data Driven AI Framework for Flexible Protein Conformational Reconstruction.bioRxiv : the preprint server for biology · 2026Article
- Predicting Pose Distribution of Protein Domains Connected by Flexible Linkers Is an Unsolved Problem.Proteins · 2026Article
- AlphaFold modeling uncovers global structural features of class I and class II fungal hydrophobins.Protein science : a publication of the Protein Society · 2025Article
- The Pseudoenzyme β-Amylase9 From Arabidopsis Activates α-Amylase3: A Possible Mechanism to Promote Stress-Induced Starch Degradation.Proteins · 2025Article
- Resolving the conformational ensemble of a membrane protein by integrating small-angle scattering with AlphaFold.PLoS computational biology · 2025Article
- Selective deuteration of an RNA:RNA complex for structural analysis using small-angle scattering.Structure (London, England : 1993) · 2025Article
- Use of AI-methods over MD simulations in the sampling of conformational ensembles in IDPs.Frontiers in molecular biosciences · 2025Review
- Selective deuteration of an RNA:RNA complex for structural analysis using small-angle scattering.bioRxiv : the preprint server for biology · 2024Article
- The pseudoenzyme β-amylase9 from Arabidopsis binds to and enhances the activity of α-amylase3: A possible mechanism to promote stress-induced starch degradation.bioRxiv : the preprint server for biology · 2024Article
- The power and pitfalls of AlphaFold2 for structure prediction beyond rigid globular proteins.Nature chemical biology · 2024Review
- Effects ofFrontiers in molecular biosciences · 2024Article
- Representing structures of the multiple conformational states of proteins.Current opinion in structural biology · 2023Review
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6 authors.
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Abstract
Accurate protein structure predictions, enabled by recent advances in machine learning algorithms, provide an entry point to probing structural mechanisms and to integrating and querying many types of biochemical and biophysical results. Limitations in such protein structure predictions can be reduced and addressed through comparison to experimental Small Angle X-ray Scattering (SAXS) data that provides protein structural information in solution. SAXS data can not only validate computational predictions, but can improve conformational and assembly prediction to produce atomic models that are consistent with solution data and biologically relevant states. Here, we describe how to obtain protein structure predictions, compare them to experimental SAXS data and improve models to reflect experimental information from SAXS data. Furthermore, we consider the potential for such experimentally-validated protein structure predictions to broadly improve functional annotation in proteins identified in metagenomics and to identify functional clustering on conserved sites despite low sequence homology.
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