ArticleGenome biology2023
Cross-phyla protein annotation by structural prediction and alignment.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 38 citations in OpenAlex.
- ProtPen combines sequence- and structure-based approaches to facilitate protein function predictions on a proteome-wide scale.bioRxiv : the preprint server for biology · 2026Article
- Structural motif search across the protein universe with Folddisco.Nature biotechnology · 2026Article
- Unveiling Putative Functions of Burkholderia pseudomallei K96243 Hypothetical Proteins Via High-Throughput Characterization of Structural Similarities.Interdisciplinary sciences, computational life sciences · 2026Article
- Prediction of eukaryotic cellular complexity in Asgard archaea using structural modelling.Nature microbiology · 2026Article
- The transformative impact of AI-enabled AlphaFold 3: evolution, current status, and future prospects in structural biology.Frontiers in artificial intelligence · 2026Review
- Functional (re)annotation ofCurrent research in structural biology · 2025Article
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- De novo discovery of conserved gene clusters in microbial genomes with Spacedust.Nature methods · 2025Article
- SARST2 high-throughput and resource-efficient protein structure alignment against massive databases.Nature communications · 2025Article
- ModelArchive: A Deposition Database for Computational Macromolecular Structural Models.Journal of molecular biology · 2025Article
- Unicore Enables Scalable and Accurate Phylogenetic Reconstruction with Structural Core Genes.Genome biology and evolution · 2025Article
- Article
- Analysis of metagenomic data.Nature reviews. Methods primers · 2025Article
- Proteomic analysis of the sponge Aggregation Factor implicates an ancient toolkit for allorecognition and adhesion in animals.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Quest for Orthologs in the Era of Biodiversity Genomics.Genome biology and evolution · 2024Review
- AlphaFold two years on: Validation and impact.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- The genome of the colonial hydroidGenome research · 2024Article
- Functional domain annotation by structural similarity.NAR genomics and bioinformatics · 2024Article
- Author Correction: Cross-phyla protein annotation by structural prediction and alignment.Genome biology · 2024Article
- Phylogenetic and functional analyses ofmSphere · 2024Article
Corrections and comments
- Erratum issued
Authors and funding
6 authors at 4 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundProtein annotation is a major goal in molecular biology, yet experimentally determined knowledge is typically limited to a few model organisms. In non-model species, the sequence-based prediction of gene orthology can be used to infer protein identity; however, this approach loses predictive power at longer evolutionary distances. Here we propose a workflow for protein annotation using structural similarity, exploiting the fact that similar protein structures often reflect homology and are more conserved than protein sequences.
resultsWe propose a workflow of openly available tools for the functional annotation of proteins via structural similarity (MorF: MorphologFinder) and use it to annotate the complete proteome of a sponge. Sponges are highly relevant for inferring the early history of animals, yet their proteomes remain sparsely annotated. MorF accurately predicts the functions of proteins with known homology in [Formula: see text] cases and annotates an additional [Formula: see text] of the proteome beyond standard sequence-based methods. We uncover new functions for sponge cell types, including extensive FGF, TGF, and Ephrin signaling in sponge epithelia, and redox metabolism and control in myopeptidocytes. Notably, we also annotate genes specific to the enigmatic sponge mesocytes, proposing they function to digest cell walls.
conclusionsOur work demonstrates that structural similarity is a powerful approach that complements and extends sequence similarity searches to identify homologous proteins over long evolutionary distances. We anticipate this will be a powerful approach that boosts discovery in numerous -omics datasets, especially for non-model organisms.
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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.