ArticleNature communications2023
Merizo: a rapid and accurate protein domain segmentation method using invariant point attention.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Proteome-wide identification of the druggable CRBN interactome.Nature biotechnology · 2026Article
- TEDLH: domain HMMs for sensitive detection of remote homologues.Bioinformatics (Oxford, England) · 2026Article
- SplitSeek-Pro: accurate prediction of splittable sites on protein structures.Nature communications · 2026Article
- DeepRank-Ab: a scoring function for antibody-antigen complexes based on geometric deep learning.Communications biology · 2026Article
- Structural genomics sheds light on protein functions and remote homologs across the insect tree of life.Cell research · 2026Article
- metaRLK 2.0: An updated database of plant receptor-like kinases developed with structure- and deep learning-based functional annotation and classification.Plant communications · 2026Article
- Family-level specialization in protein domain insertion architectures.Protein science : a publication of the Protein Society · 2026Article
- Atlas of predicted protein complex structures across kingdoms.Nature communications · 2026Article
- Multiomics combined drugs to explore the potential mechanism and treatment of ankylosing spondylitis.Journal of orthopaedic surgery and research · 2026Article
- Quest for Orthologs in the era of Data Deluge and AI: Challenges and Innovations in Orthology Prediction and Data Integration.Journal of molecular evolution · 2025Review
- A genomic atlas of the human gut virome elucidates genetic factors shaping host interactions.bioRxiv : the preprint server for biology · 2025Article
- AFragmenter: schema-free, tuneable protein domain segmentation for AlphaFold protein structures.Bioinformatics (Oxford, England) · 2025Article
- Zero-shot segmentation using embeddings from a protein language model identifies functional regions in the human proteome.PLoS computational biology · 2025Article
- Multimodal deep learning integration of cryo-EM and AlphaFold3 for high-accuracy protein structure determination.Communications chemistry · 2025Article
- SPAED: harnessing AlphaFold output for accurate segmentation of phage endolysin domains.Bioinformatics (Oxford, England) · 2025Article
- The CAGE complex: a hollow, megadalton, protein assembly in prokaryotic and eukaryotic microbes.bioRxiv : the preprint server for biology · 2025Article
- Foldclass and Merizo-search: scalable structural similarity search for single- and multi-domain proteins using geometric learning.Bioinformatics (Oxford, England) · 2025Article
- Protein sequence modelling with Bayesian flow networks.Nature communications · 2025Article
- Slice'N'Dice: maximizing the value of predicted models for structural biologists.Acta crystallographica. Section D, Structural biology · 2025Article
- Fast protein structure searching using structure graph embeddings.Bioinformatics advances · 2025Article
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3 authors.
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Abstract
The AlphaFold Protein Structure Database, containing predictions for over 200 million proteins, has been met with enthusiasm over its potential in enriching structural biological research and beyond. Currently, access to the database is precluded by an urgent need for tools that allow the efficient traversal, discovery, and documentation of its contents. Identifying domain regions in the database is a non-trivial endeavour and doing so will aid our understanding of protein structure and function, while facilitating drug discovery and comparative genomics. Here, we describe a deep learning method for domain segmentation called Merizo, which learns to cluster residues into domains in a bottom-up manner. Merizo is trained on CATH domains and fine-tuned on AlphaFold2 models via self-distillation, enabling it to be applied to both experimental and AlphaFold2 models. As proof of concept, we apply Merizo to the human proteome, identifying 40,818 putative domains that can be matched to CATH representative domains.
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