ArticleProceedings of the National Academy of Sciences of the United States of America2025
Integrative spatiotemporal modeling of biomolecular processes: Application to the assembly of the nuclear pore complex.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2025. 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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Who cites it
6 citing papers in PubMed.
- The responsive nucleus: morphological signatures of cellular state.Nucleus (Austin, Tex.) · 2026Review
- Hydrophobic interactions of FG-nucleoporins are required for dilating nuclear membrane pores into selective transport channels after mitosis.Nature structural & molecular biology · 2026Article
- RCSB Protein Data Bank: Delivering integrative structures alongside experimental structures and computed structure models.Nucleic acids research · 2026Article
- Opening the black box: insights into ubiquitin-mediated control of innate antiviral immunity and AI-enhanced therapeutics.Frontiers in immunology · 2026Review
- Hydrophobic interactions of FG-nucleoporins are required for dilating nuclear membrane pores into selective transport channels after mitosis.bioRxiv : the preprint server for biology · 2025Article
- Tutorial on integrative spatiotemporal modeling by integrative modeling platform.Protein science : a publication of the Protein Society · 2025Article
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Abstract
Dynamic processes involving biomolecules are essential for the function of the cell. Here, we introduce an integrative method for computing models of these processes based on multiple heterogeneous sources of information, including time-resolved experimental data and physical models of dynamic processes. First, for each time point, a set of coarse models of compositional and structural heterogeneity is computed (heterogeneity models). Second, for each heterogeneity model, a set of static integrative structure models is computed (a snapshot model). Finally, these snapshot models are selected and connected into a series of trajectories that optimize the likelihood of both the snapshot models and transitions between them (a trajectory model). The method is demonstrated by application to the assembly process of the human nuclear pore complex in the context of the reforming nuclear envelope during mitotic cell division, based on live-cell correlated electron tomography, bulk fluorescence correlation spectroscopy-calibrated quantitative live imaging, and a structural model of the fully assembled nuclear pore complex. Modeling of the assembly process improves the model precision over static integrative structure modeling alone. The method is applicable to a wide range of time-dependent systems in cell biology and is available to the broader scientific community through an implementation in the open source
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