ArticleNature communications2025
Deep indel mutagenesis reveals the impact of amino acid insertions and deletions on protein stability and function.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 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
22 citing papers in PubMed.
- A unified predictor of protein stability changes across all mutation typesChemical science · 2026Article
- A NovelInternational journal of molecular sciences · 2026Article
- MuRaL-indel: a deep learning framework for building insertion and deletion mutation rate maps.Briefings in bioinformatics · 2026Article
- Massively parallel quantification of mutational impact on IAPP amyloid formation.Nature communications · 2026Article
- Decoding epitope immunodominance in HIV Env using cryoEM and machine learning.bioRxiv : the preprint server for biology · 2026Article
- Mapping the phenotypic landscape of a transcriptional repressor using deep mutational scanning and growth-based quantitative sequencing.Nucleic acids research · 2026Article
- Engineering a Bright Near-Infrared Fluorescent Protein by Screening a Comprehensive Phenotypic Landscape.bioRxiv : the preprint server for biology · 2025Article
- Analysis of insertion/deletion variation of litter size in Guizhou black goat.Tropical animal health and production · 2025Article
- Graph attention with structural features improves the generalizability of identifying functional sequences at a protein interface.bioRxiv : the preprint server for biology · 2025Article
- Scaling DNA synthesis with a microchip-based massively parallel synthesis system.Nature biotechnology · 2025Article
- Uncovering differential tolerance to deletions versus substitutions with a protein language model.Cell systems · 2025Article
- Deep-learning structure elucidation from single-mutant deep mutational scanning.Nature communications · 2025Article
- Sequence Variation and In Silico Protein Characterization ofInternational journal of molecular sciences · 2025Article
- Indels allow antiviral proteins to evolve functional novelty inaccessible by missense mutations.Cell genomics · 2025Article
- Shared-weight graph framework for comprehensive protein stability prediction across diverse mutation types.Briefings in bioinformatics · 2025Article
- Article
- Article
- Amino acid sequence encodes protein abundance shaped by protein stability at reduced synthesis cost.Protein science : a publication of the Protein Society · 2025Article
- Structural and energetic analysis of stabilizing indel mutations.bioRxiv : the preprint server for biology · 2024Article
- Comprehensive deletion scan of anti-CRISPR AcrIIA4 reveals essential and dispensable domains for Cas9 inhibition.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Amino acid insertions and deletions (indels) are an abundant class of genetic variants. However, compared to substitutions, the effects of indels on protein stability are not well understood. To better understand indels here we analyse new and existing large-scale deep indel mutagenesis (DIM) of structurally diverse proteins. The effects of indels on protein stability vary extensively among and within proteins and are not well predicted by existing computational methods. To address this shortcoming we present INDELi, a series of models that combine experimental or predicted substitution effects and secondary structure information to provide good prediction of the effects of indels on both protein stability and pathogenicity. Moreover, quantifying the effects of indels on protein-protein interactions suggests that insertions can be an important class of gain-of-function variants. Our results provide an overview of the impact of indels on proteins and a method to predict their effects genome-wide.
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.