ArticleBioinformatics (Oxford, England)2023
PROSTATA: a framework for protein stability assessment using transformers.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Persistent sheaf Laplacian analysis of protein stability and solubility changes upon mutation.Protein science : a publication of the Protein Society · 2026Article
- Prot-ΔΔG: Prediction of protein-protein binding affinity changes upon mutations with pre-training strategies.Journal of computer-aided molecular design · 2026Article
- MuFaDDG: a sequence-based multiscale feature fusion framework for protein stability changes prediction.Bioinformatics (Oxford, England) · 2026Article
- JanusDDG: a physics-informed neural network for sequence-based protein stability via two-fronts attention.Communications biology · 2026Article
- Generalizable and scalable protein stability prediction with rewired protein generative models.Nature communications · 2025Article
- DDGWizard: Integration of feature calculation resources for analysis and prediction of changes in protein thermostability upon point mutations.PLoS computational biology · 2025Article
- Article
- Predicting protein stability changes upon mutations with dual-view ensemble learning from single sequence.Briefings in bioinformatics · 2025Article
- AFToolkit: a framework for molecular modeling of proteins with AlphaFold-derived representations.Briefings in bioinformatics · 2025Article
- OrgNet: orientation-gnostic protein stability assessment using convolutional neural networks.Bioinformatics (Oxford, England) · 2025Article
- Exploring Evolution to Uncover Insights Into Protein Mutational Stability.Molecular biology and evolution · 2025Article
- DDGemb: predicting protein stability change upon single- and multi-point variations with embeddings and deep learning.Bioinformatics (Oxford, England) · 2024Article
- ESM-scan-A tool to guide amino acid substitutions.Protein science : a publication of the Protein Society · 2024Article
- PRITrans: A Transformer-Based Approach for the Prediction of the Effects of Missense Mutation on Protein-RNA Interactions.International journal of molecular sciences · 2024Article
- Molecular Modeling and In Vitro Functional Analysis of the RGS12 PDZ Domain Variant Associated with High-Penetrance Familial Bipolar Disorder.International journal of molecular sciences · 2024Article
- BenchStab: a tool for automated querying of web-based stability predictors.Bioinformatics (Oxford, England) · 2024Article
- An end-to-end framework for the prediction of protein structure and fitness from single sequence.Nature communications · 2024Article
- Stability Oracle: a structure-based graph-transformer framework for identifying stabilizing mutations.Nature communications · 2024Article
- Enhancing predictions of protein stability changes induced by single mutations using MSA-based language models.Bioinformatics (Oxford, England) · 2024Article
- Transfer learning to leverage larger datasets for improved prediction of protein stability changes.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
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Authors and funding
8 authors.
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No grant is acknowledged in the PubMed record.
Abstract
motivationAccurate prediction of change in protein stability due to point mutations is an attractive goal that remains unachieved. Despite the high interest in this area, little consideration has been given to the transformer architecture, which is dominant in many fields of machine learning.
resultsIn this work, we introduce PROSTATA, a predictive model built in a knowledge-transfer fashion on a new curated dataset. PROSTATA demonstrates advantage over existing solutions based on neural networks. We show that the large improvement margin is due to both the architecture of the model and the quality of the new training dataset. This work opens up opportunities to develop new lightweight and accurate models for protein stability assessment. AVAILABILITY AND IMPLEMENTATION: PROSTATA is available at https://github.com/AIRI-Institute/PROSTATA and https://prostata.airi.net.
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