ArticleNature communications2025
Modeling protein conformational ensembles by guiding AlphaFold2 with Double Electron Electron Resonance (DEER) distance distributions.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Enhanced Sampling of Protein Conformations in AlphaFold3 with Repulsive Bias in the Diffusion Generative Model.JACS Au · 2026Article
- Multiple quantumScience advances · 2026Article
- EPR spectroscopy 80 years after its discovery.Science advances · 2026Review
- New paradigm of q-CAR drug development targeting disease-specific protein conformations.npj drug discovery · 2026Review
- ESMDynamic: Fast and accurate prediction of protein dynamic contact maps from single sequences.Nature communications · 2026Article
- Proton-coupled alternating access in a versatile mycobacterial Spns drug transporter.Research square · 2026Article
- Comprehensive Tutorial for Computational Methods of Protein Structure Prediction Incorporating Mass Spectrometry Data.Mass spectrometry reviews · 2026Review
- Proton-coupled alternating access in a versatile mycobacterial Spns drug transporter.bioRxiv : the preprint server for biology · 2026Article
- AI-Physics-Experiment Trinity for Integrated Protein Dynamics Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Incorporating Surfaced-Induced Dissociation Mass Spectrometry Data into an AlphaFold-derived deep learning network improves protein structure prediction.bioRxiv : the preprint server for biology · 2026Article
- Distance-Restraint-Guided Diffusion Models for Sampling Protein Conformational Changes and Ligand Dissociation Pathways.Journal of chemical theory and computation · 2026Article
- Large-scale protein conformational transitions revealed by weighted ensemble simulations and EPR.Chemical science · 2026Article
- Bayesian-Steered Structure Prediction of Mechanical Biomolecules Using Twisted Diffusion.bioRxiv : the preprint server for biology · 2026Article
- Recent advances in quantifying protein conformational ensembles with dipolar EPR spectroscopy.Current opinion in structural biology · 2025Review
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Authors and funding
5 authors.
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Abstract
We describe a modified version of AlphaFold2 that incorporates experimental distance distributions into the network architecture for protein structure prediction. Harnessing the OpenFold platform, we fine-tune AlphaFold2 on structurally dissimilar proteins to explicitly model distance distributions between spin labels determined from Double Electron-Electron Resonance (DEER) spectroscopy. We benchmark the performance of the modified AlphaFold2, refer to as DEERFold, in switching the predicted conformations of a set of membrane transporters using experimental DEER distance distributions. Guided by sparse sets of simulated distance distributions, we showcase the generality of DEERFold in predicting conformational ensembles on a large benchmark set of water soluble and membrane proteins. We find that the intrinsic performance of AlphaFold2 substantially reduces the number of required distributions and the accuracy of their widths needed to drive conformational selection thereby increasing the experimental throughput. The blueprint of DEERFold can be generalized to other experimental methods where distance constraints can be represented by distributions.
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