ArticleProtein science : a publication of the Protein Society2026
Compartment-guided assembly of large-scale molecular models with Bentopy.
Article in Protein science : a publication of the Protein Society, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- The physicochemical design, structure and permeability of the JCVI-syn3A minimal cell membrane.Nature communications · 2026Article
- The molecular basis of mitochondrial crista formation by the MIC10 complex.Science advances · 2026Article
- Martini 3 Metabolome.Journal of chemical theory and computation · 2026Article
- Compartment-guided assembly of large-scale molecular models with Bentopy.Protein science : a publication of the Protein Society · 2026Article
- Structural and functional implications of phase separation of membrane protein LacY in Escherichia coli.Nature communications · 2026Article
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Authors and funding
7 authors.
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Abstract
Molecular dynamics simulations of whole cells and organelles aim to transform cell biology by providing a molecular view into the crowded cellular environment. However, constructing suitable starting configurations remains a major bottleneck due to their size and complexity. We present bentopy, a workflow for building cellular-scale models ready for simulation. Bentopy uses a voxel-based spatial representation to efficiently pack molecules into arbitrarily complex compartments. The modular design facilitates the assembly of molecular models containing millions of molecules in minutes on standard workstations. We demonstrate bentopy through three experimentally informed models spanning multiple biological scales. A JCVI-Syn3A whole-cell model combines existing membrane and chromosome structures with diverse cytosolic components. A mitochondrion model integrates cryo-electron tomography maps with spatially resolved proteomics and metabolomics data. An atomistic SARS-CoV-2 virion inside a respiratory aerosol demonstrates bentopy's capability to pack at both atomistic and coarse-grained resolution. Together, these applications establish bentopy as a workflow for constructing simulation-ready models at the cellular scale.
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Registered trials
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