ArticleStructure (London, England : 1993)2024
DomainFit: Identification of protein domains in cryo-EM maps at intermediate resolution using AlphaFold2-predicted models.
Article in Structure (London, England : 1993), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed.
- In situ structure of the poxvirus portal complex.Nature · 2026Article
- SPACA9 and MNMIP1 bridge the seam of spermatid manchette microtubules.The EMBO journal · 2026Article
- Automated assembly of protein complexes from cryo-EM maps with structure-informed Monte Carlo Tree Search.bioRxiv : the preprint server for biology · 2026Article
- Visual exoproteomics ofbioRxiv : the preprint server for biology · 2026Article
- Structure first - exploration and discovery with cryo-electron microscopy.Journal of cell science · 2026Review
- Atomic models of the Toxoplasma cell invasion machinery.Nature structural & molecular biology · 2026Article
- Distance-AF improves predicted protein structure models by AlphaFold2 with user-specified distance constraints.Communications biology · 2025Article
- Bridging the gap: how sperm's core structure explains male infertility.Cell research · 2025Article
- Heterogeneity of radial spoke components in Tetrahymena cilia.Cellular and molecular life sciences : CMLS · 2025Article
- In situ structure of the mouse sperm central apparatus reveals mechanistic insights into asthenozoospermia.Cell research · 2025Article
- Structure of the ciliary tip central pair reveals the unique role of the microtubule-seam binding protein SPEF1.Current biology : CB · 2025Article
- CryoEM structure of thebioRxiv : the preprint server for biology · 2025Article
- Structure of AcMNPV nucleocapsid reveals DNA portal organization and packaging apparatus of circular dsDNA baculovirus.Nature communications · 2025Article
- Structures of Native Doublet Microtubules from Trichomonas vaginalis Reveal Parasite-Specific Proteins.Nature communications · 2025Article
- A ternary complex of MIPs in the A-tubule of basal bodies and axonemes depends on RIB22 and the EF-hand domain of RIB72A inMolecular biology of the cell · 2025Article
- Advancing structure modeling from cryo-EM maps with deep learning.Biochemical Society transactions · 2025Review
- Editorial: Advances in cilia and flagella research.Frontiers in cell and developmental biology · 2025Article
- The Structure of Cilium Inner Junctions Revealed by Electron Cryo-tomography.bioRxiv : the preprint server for biology · 2024Article
- Structures of Native Doublet Microtubules fromResearch square · 2024Article
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Abstract
Cryoelectron microscopy (cryo-EM) has revolutionized the structural determination of macromolecular complexes. With the paradigm shift to structure determination of highly complex endogenous macromolecular complexes ex vivo and in situ structural biology, there are an increasing number of structures of native complexes. These complexes often contain unidentified proteins, related to different cellular states or processes. Identifying proteins at resolutions lower than 4 Å remains challenging because side chains cannot be visualized reliably. Here, we present DomainFit, a program for semi-automated domain-level protein identification from cryo-EM maps, particularly at resolutions lower than 4 Å. By fitting domains from AlphaFold2-predicted models into cryo-EM maps, the program performs statistical analyses and attempts to identify the domains and protein candidates forming the density. Using DomainFit, we identified two microtubule inner proteins, one of which contains a CCDC81 domain and is exclusively localized in the proximal region of the doublet microtubule in Tetrahymena thermophila.
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