ArticleStructure (London, England : 1993)2023
Computational modeling and prediction of deletion mutants.
Article in Structure (London, England : 1993), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
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- Fungal Rutinosidase─Engineering of a Side Tunnel Steers Its Transglycosylation Potential.Journal of agricultural and food chemistry · 2026Article
- CASP16 Protein Monomer Structure Prediction Assessment.Proteins · 2026Article
- Adversarial Sequence Mutations in AlphaFold and ESMFold Reveal Nonphysical Structural Invariance, Confidence Failures, and Concerns for Protein Design.Computational and structural biotechnology journal · 2026Article
- Energetic and structural control of polyspecificity in a multidrug transporter.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Thrombomodulin is essential for recombinant Fc-fusion protein production in Chinese hamster ovary cells via multiple signaling pathways.Journal of biological engineering · 2025Article
- Uncovering differential tolerance to deletions versus substitutions with a protein language model.Cell systems · 2025Article
- FBXO22 deficiency defines a pleiotropic syndrome of growth restriction and multi-system anomalies associated with a unique epigenetic signature.American journal of human genetics · 2025Article
- Integration of protein stability and AlphaMissense scores improves bioinformatic impact prediction for p53 missense and in-frame amino acid deletion variants.American journal of human genetics · 2025Article
- Modulation of the tumor immune microenvironment by Interferon Regulatory Factor 8 enhances immunotherapy in lung adenocarcinoma.Scientific reports · 2025Article
- Sam-Sam Association Between EphA2 and SASH1: In Silico Studies of Cancer-Linked Mutations.Molecules (Basel, Switzerland) · 2025Article
- LINE-1 transposition into murine Thyroglobulin results in congenital thyroid dysplasia.PloS one · 2025Article
- Insertion-Deletion Events Are Depleted in Protein Regions with Predicted Secondary Structure.Genome biology and evolution · 2024Article
- Cancer-Related Mutations in the Sam Domains of EphA2 Receptor and Ship2 Lipid Phosphatase: A Computational Study.Molecules (Basel, Switzerland) · 2024Article
- Dark nanodiscs for evaluating membrane protein thermostability by differential scanning fluorimetry.Biophysical journal · 2024Article
Corrections and comments
- Commented on byMind the gap.2023
Authors and funding
8 authors.
Funding
Abstract
In-frame deletion mutations can result in disease. The impact of these mutations on protein structure and subsequent functional changes remain understudied, partially due to the lack of comprehensive datasets including a structural readout. In addition, the recent breakthrough in structure prediction through deep learning demands an update of computational deletion mutation prediction. In this study, we deleted individually every residue of a small α-helical sterile alpha motif domain and investigated the structural and thermodynamic changes using 2D NMR spectroscopy and differential scanning fluorimetry. Then, we tested computational protocols to model and classify observed deletion mutants. We show a method using AlphaFold2 followed by RosettaRelax performs the best overall. In addition, a metric containing pLDDT values and Rosetta ΔΔG is most reliable in classifying tolerated deletion mutations. We further test this method on other datasets and show they hold for proteins known to harbor disease-causing deletion mutations.
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