ArticleNature communications2024
Structure prediction of alternative protein conformations.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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Who cites it
65 citing papers in PubMed.
- The Advantages of AI for Computational Protein Studies and Looking Ahead at the Next Challenges: Single Structures Are Not Enough.Journal of molecular biology · 2026Review
- Several multiple sequence alignment-perturbing methods enhance AlphaFold3 sampling of alternative protein states.Communications chemistry · 2026Article
- Hierarchical discrete representations for coarse-to-fine protein conformation generation.Bioinformatics (Oxford, England) · 2026Article
- Explainable AI reveals the allosteric blind spot in protein-ligand binding predictions.Cell reports. Physical science · 2026Article
- PETIMOT: a novel framework for inferring protein motions from sparse data using SE(3)-equivariant graph neural networks.Acta crystallographica. Section D, Structural biology · 2026Article
- AlphaFold reveals but sometimes distorts an organizational principle of protein folding.bioRxiv : the preprint server for biology · 2026Article
- Benchmarking AI Protein Structure Predictors Reveals a Persistent Bias in Multi-State Proteins.bioRxiv : the preprint server for biology · 2026Article
- The influence of ligands on AlphaFold3 prediction of cryptic pockets.Communications biology · 2026Article
- DeepPath: overcoming data scarcity for protein transition pathway prediction using physics-based deep learning.Chemical science · 2026Article
- Exploring the conformational landscape of adenylate kinase and beyond with protein folding models.Scientific reports · 2026Article
- More protein-ligand data are needed for AlphaFold-like models to enable drug discovery.Current opinion in structural biology · 2026Review
- Thermodynamic prediction of RNA cellular activity from sequence via conformational ensembles.Cell · 2026Article
- The latest AI breakthroughs in structural biology: protein binder design and conformational state prediction.Communications biology · 2026Article
- ConforFold recovers alternative protein conformations beyond MSA subsampling.Protein science : a publication of the Protein Society · 2026Article
- Fold-Switching Proteins.Annual review of biophysics · 2026Review
- Hidden structural states of proteins revealed by conformer selection.Nature communications · 2026Article
- Comparative study of two xanthan gum glycosyltransferases combining AI structure predictions and molecular modeling.bioRxiv : the preprint server for biology · 2026Article
- Bias in the AlphaFold3 prediction of ligand-induced domain motion in enzymes.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Generating Dynamic Structures Through Physics-Based Sampling of Predicted Inter-Residue Geometries.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Comparative Analysis of AlphaFold2 Models and Intrinsic Disorder Illuminates Structural Divergence as a Symptom of Functional Divergence Across the Calmodulin Superfamily.Journal of molecular evolution · 2026Article
5 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
Funding
Abstract
Proteins are dynamic molecules whose movements result in different conformations with different functions. Neural networks such as AlphaFold2 can predict the structure of single-chain proteins with conformations most likely to exist in the PDB. However, almost all protein structures with multiple conformations represented in the PDB have been used while training these models. Therefore, it is unclear whether alternative protein conformations can be genuinely predicted using these networks, or if they are simply reproduced from memory. Here, we train a structure prediction network, Cfold, on a conformational split of the PDB to generate alternative conformations. Cfold enables efficient exploration of the conformational landscape of monomeric protein structures. Over 50% of experimentally known nonredundant alternative protein conformations evaluated here are predicted with high accuracy (TM-score > 0.8).
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.