ArticleProtein science : a publication of the Protein Society2025
Predicting absolute protein folding stability using generative models.
Article in Protein science : a publication of the Protein Society, 2025. 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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Who cites it
23 citing papers in PubMed.
- RINAMI: Residue-attributed interpretable neural network for predicting absolute folding free energy by merging structure and sequence information.Protein science : a publication of the Protein Society · 2026Article
- Accurate protein stability prediction for small domains using mega-scale experiments.bioRxiv : the preprint server for biology · 2026Article
- Protein Stability, Turnover Kinetics, and Abundance Constrain the Scaling of Protein Interaction Networks.bioRxiv : the preprint server for biology · 2026Article
- ANYI: The ANnotated Yeast Interactome.bioRxiv : the preprint server for biology · 2026Article
- Supervised learning of protein variant effects across large-scale mutagenesis datasets.Protein science : a publication of the Protein Society · 2026Article
- Reliable repurposing of the antibody interactome inside the cell.Nature communications · 2026Article
- Protein folding stability estimation with explicit consideration of unfolded states.Nature communications · 2026Article
- Stable de novo protein design via joint conformational landscape and sequence optimization.Nature communications · 2025Article
- Generalizable and scalable protein stability prediction with rewired protein generative models.Nature communications · 2025Article
- Supervised Learning of Protein Melting Temperature: Cross-Species vs. Species-Specific Prediction.Proteins · 2025Article
- Prebiotically Plausible Peptides can Self-assemble into β-rich Nanostructures.bioRxiv : the preprint server for biology · 2025Article
- Article
- Accurate Prediction of Protein Tertiary and Quaternary Stability Using Fine-Tuned Protein Language Models and Free Energy Perturbation.International journal of molecular sciences · 2025Article
- Unifying perspectives on the activity and genotypic targeting of pharmacological chaperones.The Journal of biological chemistry · 2025Review
- Statistical Thermodynamics of the Protein Ensemble: Mediating Function and Evolution.Annual review of biophysics · 2025Review
- Prediction of phase-separation propensities of disordered proteins from sequence.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Aminoacyl-tRNA synthetase urzymes optimized by deep learning behave as a quasispecies.Structural dynamics (Melville, N.Y.) · 2025Article
- Large-scale energy decomposition for the analysis of protein stability.Cell stress & chaperones · 2025Article
- Protein stability models fail to capture epistatic interactions of double point mutations.Protein science : a publication of the Protein Society · 2025Article
- Predicting absolute protein folding stability using generative models.Protein science : a publication of the Protein Society · 2025Article
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Authors and funding
3 authors.
Funding
Abstract
While there has been substantial progress in our ability to predict changes in protein stability due to amino acid substitutions, progress has been slower in methods to predict the absolute stability of a protein. Here, we show how a generative model for protein sequence can be leveraged to predict absolute protein stability. We benchmark our predictions across a broad set of proteins and find a mean error of 1.5 kcal/mol and a correlation coefficient of 0.7 for the absolute stability across a range of natural, small- to medium-sized proteins up to ca. 150 amino acid residues. We analyze current limitations and future directions including how such a model may be useful for predicting conformational free energies. Our approach is simple to use and freely available at an online implementation available via https://github.com/KULL-Centre/_2024_cagiada_stability.
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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.