ArticleJournal of chemical theory and computation2024
Approximating Projections of Conformational Boltzmann Distributions with AlphaFold2 Predictions: Opportunities and Limitations.
Article in Journal of chemical theory and computation, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed.
- Biasing Conformational Sampling in AlphaFold 3 and Boltz-2 via Pair Representation Scaling.Journal of chemical information and modeling · 2026Article
- AlphaFold reveals but sometimes distorts an organizational principle of protein folding.bioRxiv : the preprint server for biology · 2026Article
- VUStruct: A compute pipeline for high throughput and personalized structural biology.PLoS computational biology · 2026Article
- Unlocking hidden biomolecular conformational landscapes in diffusion models at inference time.ArXiv · 2026Article
- Unfreezing structural biology for drug discovery.Nature chemical biology · 2026Review
- Heterogeneous Folding Intermediates Govern the Conformational Pathway of the RNA Recognition Motif Domain of the Ewing Sarcoma Protein.Biomolecules · 2025Article
- Article
- Decomposition Analysis of Theoretical Raman Spectra for Efficient Interpretation of Experimental Spectra of Thin-Film Functional Materials.International journal of molecular sciences · 2025Article
- The Ensemble Basis of Allostery and Function: Insights from Models of Local Unfolding.Journal of molecular biology · 2025Review
- Recent advances in quantifying protein conformational ensembles with dipolar EPR spectroscopy.Current opinion in structural biology · 2025Review
- Structure Prediction of Alternate Frame Folding Systems with AlphaFold3.Journal of chemical information and modeling · 2025Article
- Article
- Protein Modeling with DEER Spectroscopy.Annual review of biophysics · 2025Review
- Harnessing AlphaFold to reveal hERG channel conformational state secrets.bioRxiv : the preprint server for biology · 2025Article
- Physics-based modeling in the new era of enzyme engineering.Nature computational science · 2025Review
- Article
- Use of AI-methods over MD simulations in the sampling of conformational ensembles in IDPs.Frontiers in molecular biosciences · 2025Review
- Unlocking hidden biomolecular conformational landscapes in diffusion models at inference time.Advances in neural information processing systems · 2025Article
- AlphaFold2-Based Characterization of Apo and Holo Protein Structures and Conformational Ensembles Using Randomized Alanine Sequence Scanning Adaptation: Capturing Shared Signature Dynamics and Ligand-Induced Conformational Changes.International journal of molecular sciences · 2024Article
- ESM-scan-A tool to guide amino acid substitutions.Protein science : a publication of the Protein Society · 2024Article
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Abstract
Protein thermodynamics is intimately tied to biological function and can enable processes such as signal transduction, enzyme catalysis, and molecular recognition. The relative free energies of conformations that contribute to these functional equilibria evolved for the physiology of the organism. Despite the importance of these equilibria for understanding biological function and developing treatments for disease, computational and experimental methods capable of quantifying the energetic determinants of these equilibria are limited to systems of modest size. Recently, it has been demonstrated that the artificial intelligence system AlphaFold2 can be manipulated to produce structurally valid protein conformational ensembles. Here, we extend these studies and explore the extent to which AlphaFold2 contact distance distributions can approximate projections of the conformational Boltzmann distributions. For this purpose, we examine the joint probability distributions of inter-residue contact distances along functionally relevant collective variables of several protein systems. Our studies suggest that AlphaFold2 normalized contact distance distributions can correlate with conformation probabilities obtained with other methods but that they suffer from peak broadening. We also find that the AlphaFold2 contact distance distributions can be sensitive to point mutations. Overall, we anticipate that our findings will be valuable as the community seeks to model the thermodynamics of conformational changes in large biomolecular systems.
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