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However, constructing suitable starting configurations remains a major bottleneck due to their size and complexity. We present\n                    <jats:italic>bentopy<\/jats:italic>\n                    , a workflow for building cellular\u2010scale models ready for simulation.\n                    <jats:italic>Bentopy<\/jats:italic>\n                    uses a voxel\u2010based 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\n                    <jats:italic>bentopy<\/jats:italic>\n                    through three experimentally informed models spanning multiple biological scales. A JCVI\u2010Syn3A whole\u2010cell model combines existing membrane and chromosome structures with diverse cytosolic components. A mitochondrion model integrates cryo\u2010electron tomography maps with spatially resolved proteomics and metabolomics data. An atomistic SARS\u2010CoV\u20102 virion inside a respiratory aerosol demonstrates\n                    <jats:italic>bentopy<\/jats:italic>\n                    's capability to pack at both atomistic and coarse\u2010grained resolution. Together, these applications establish\n                    <jats:italic>bentopy<\/jats:italic>\n                    as a workflow for constructing simulation\u2010ready models at the cellular scale.\n                  <\/jats:p>","DOI":"10.1002\/pro.70480","type":"journal-article","created":{"date-parts":[[2026,2,12]],"date-time":"2026-02-12T11:12:54Z","timestamp":1770894774000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Compartment\u2010guided assembly of large\u2010scale molecular models with\n                    <i>Bentopy<\/i>"],"prefix":"10.1002","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0009-0005-2382-8913","authenticated-orcid":false,"given":"M. S. 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