ArticlePLoS computational biology2024
Structure-aware annotation of leucine-rich repeat domains.
Article in PLoS computational biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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6 citing papers in PubMed.
- Integrative sequence-structure analysis reveals hidden WD40 domains forming stable β-propeller folds with potential biological functions in plants.Plant communications · 2026Article
- Machine Learning-Based Genome-Wide Association Study Reveals Genetic Loci Associated with Body Measurement Traits in Yili Horses.Animals : an open access journal from MDPI · 2026Article
- Research advances on NLRP3 inflammasomes in organ transplantation.Frontiers in immunology · 2026Review
- Designing novel solenoid proteins with in silico evolution.Communications chemistry · 2025Article
- mamp-ml: A deep learning approach to epitope immunogenicity in plants.bioRxiv : the preprint server for biology · 2025Article
- Mining SNP loci and candidate genes for sheath blight resistance inFrontiers in plant science · 2025Article
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5 authors.
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Abstract
Protein domain annotation is typically done by predictive models such as HMMs trained on sequence motifs. However, sequence-based annotation methods are prone to error, particularly in calling domain boundaries and motifs within them. These methods are limited by a lack of structural information accessible to the model. With the advent of deep learning-based protein structure prediction, existing sequenced-based domain annotation methods can be improved by taking into account the geometry of protein structures. We develop dimensionality reduction methods to annotate repeat units of the Leucine Rich Repeat solenoid domain. The methods are able to correct mistakes made by existing machine learning-based annotation tools and enable the automated detection of hairpin loops and structural anomalies in the solenoid. The methods are applied to 127 predicted structures of LRR-containing intracellular innate immune proteins in the model plant Arabidopsis thaliana and validated against a benchmark dataset of 172 manually-annotated LRR domains.
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