ArticleFrontiers in bioengineering and biotechnology2020
Prediction of Protein Mutational Free Energy: Benchmark and Sampling Improvements Increase Classification Accuracy.
Article in Frontiers in bioengineering and biotechnology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers.
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Who cites it
69 citing papers in PubMed.
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- Aligning protein-generative models to experimental fitness with ProteinDPO.Nature methods · 2026Article
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- Advances and opportunities for computational interrogation of plant proteins.The Plant journal : for cell and molecular biology · 2026Review
- VUStruct: A compute pipeline for high throughput and personalized structural biology.PLoS computational biology · 2026Article
- MAVISp: A modular structure-based framework for protein variant effects.Protein science : a publication of the Protein Society · 2026Article
- Negative design enables cell-free expression and folding of designed transmembrane β-barrels.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Using experimental results of protein design to guide biomolecular energy-function development.PLoS computational biology · 2026Article
- Machine learning identifies novel signatures of antifungal drug resistance in Saccharomycotina yeasts.PLoS genetics · 2026Article
- Overcoming extrapolation challenges of deep learning by incorporating physics in protein sequence-function modeling.PLoS computational biology · 2026Article
- CircadianiScience · 2026Article
- Computational design of constitutively active mutants of Dopamine D2 receptor inspired by ligand-independent activation mechanisms.BMC biology · 2026Article
- Study of POLR3A variants in a family trio suggests mutation-specific pathogenetic mechanisms: insights from integrative OMIC approaches.Cell communication and signaling : CCS · 2026Article
- SNUPN-Related Muscular Dystrophy: Novel Phenotypic, Pathological and Functional Protein Insights.Annals of clinical and translational neurology · 2026Article
- Protein folding stability estimation with explicit consideration of unfolded states.Nature communications · 2026Article
9 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
Abstract
Software to predict the change in protein stability upon point mutation is a valuable tool for a number of biotechnological and scientific problems. To facilitate the development of such software and provide easy access to the available experimental data, the ProTherm database was created. Biases in the methods and types of information collected has led to disparity in the types of mutations for which experimental data is available. For example, mutations to alanine are hugely overrepresented whereas those involving charged residues, especially from one charged residue to another, are underrepresented. ProTherm subsets created as benchmark sets that do not account for this often underrepresent tense certain mutational types. This issue introduces systematic biases into previously published protocols' ability to accurately predict the change in folding energy on these classes of mutations. To resolve this issue, we have generated a new benchmark set with these problems corrected. We have then used the benchmark set to test a number of improvements to the point mutation energetics tools in the Rosetta software suite.
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