ArticleNucleic acids research2023
DDMut: predicting effects of mutations on protein stability using deep learning.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 143 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
143 citing papers in PubMed.
- Structural and functional consequences of IL33 and IL1RL1 coding variants on IL-33/ST2 signaling.Genes and immunity · 2026Article
- Sexual Dimorphism and Intraspecific Toxin Variation in Crotalus durissus terrificus Venom: Insights from Proteomics, Peptidomics, and Structural Modeling.Journal of proteome research · 2026Article
- Computational identification and characterization of high-risk human KRAS nsSNPs: Impacting structure, ligand binding, and cancer prognosis.Journal, genetic engineering & biotechnology · 2026Article
- A dominant mutation in tomato DNA POLYMERASE DELTA 1 causes geminivirus DNA replication catastrophe.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Article
- In Silico Prioritization of Variants of Uncertain Significance in ABCA4 Reveals Conserved Functional Motifs.Research square · 2026Article
- A de novo NR2F1 c.330 C > A variant in Bosch-Boonstra-Schaaf optic atrophy syndrome presenting with early-onset developmental and epileptic encephalopathy.Molecular biology reports · 2026Article
- Contractility Drives Cardiomyocyte Maturation and the Response to Nanopatterns.Circulation research · 2026Article
- A novel IDS variant associated with an isolated ocular phenotype in Hunter syndrome.Documenta ophthalmologica. Advances in ophthalmology · 2026Article
- SARS-CoV-2 Infection-Induced Alterations in ADAR Editing Patterns Differ Between Patients Who Developed Critical Compared to Non-Critical COVID-19.International journal of molecular sciences · 2026Article
- Unheralded high MHC class II polymorphism in the abundant Atlantic herring resolved by long-read sequencing.Science advances · 2026Article
- Diagnostic utility of clinical genome reanalysis in rare pediatric disorders using long-read sequencing.HGG advances · 2026Article
- LoMuS: low-rank adaptation with sequence multi-representation improves protein stability prediction.Bioinformatics (Oxford, England) · 2026Article
- High-throughput ligand discovery in living cells using the cellular protein stability enhancement assay.Acta pharmaceutica Sinica. B · 2026Article
- Decoding variants of uncertain significance in systemic autoinflammatory diseases.Nature reviews. Rheumatology · 2026Review
- Mechanism of RACK1-dependent ZAKα activation at stalled and collided ribosomes.Molecular cell · 2026Article
- A histidine switch controls the pH-responsive self-assembly of a helical protein filament.bioRxiv : the preprint server for biology · 2026Article
- Discovery of regulatory complexes in Arabidopsis via protein-metabolite mapping during Pseudomonas infection.Plant physiology · 2026Article
- dUTPase is essential in zebrafish development and possesses several single-nucleotide variants with pronounced structural and functional consequences.FEBS open bio · 2026Article
- Alanine scanning of the yeast killer toxin K2 reveals key residues for activity, gain-of-function variants, and supports prediction of precursor processing and 3D structure.Journal of structural biology: X · 2026Article
83 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Understanding the effects of mutations on protein stability is crucial for variant interpretation and prioritisation, protein engineering, and biotechnology. Despite significant efforts, community assessments of predictive tools have highlighted ongoing limitations, including computational time, low predictive power, and biased predictions towards destabilising mutations. To fill this gap, we developed DDMut, a fast and accurate siamese network to predict changes in Gibbs Free Energy upon single and multiple point mutations, leveraging both forward and hypothetical reverse mutations to account for model anti-symmetry. Deep learning models were built by integrating graph-based representations of the localised 3D environment, with convolutional layers and transformer encoders. This combination better captured the distance patterns between atoms by extracting both short-range and long-range interactions. DDMut achieved Pearson's correlations of up to 0.70 (RMSE: 1.37 kcal/mol) on single point mutations, and 0.70 (RMSE: 1.84 kcal/mol) on double/triple mutants, outperforming most available methods across non-redundant blind test sets. Importantly, DDMut was highly scalable and demonstrated anti-symmetric performance on both destabilising and stabilising mutations. We believe DDMut will be a useful platform to better understand the functional consequences of mutations, and guide rational protein engineering. DDMut is freely available as a web server and API at https://biosig.lab.uq.edu.au/ddmut.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.