Showcase models for Bentopy

This is a record of the models used to showcase bentopy. These models demonstrate how bentopy's pack, render, merge, and solvate operations can be used to create very large, complex models. The models in this record are described in: Westendorp MSS, Stevens JA, Brown CM, Dommer AC, Wassenaar TA, Bruininks BMH, and Marrink SJ. Compartment-guided assembly of large-scale molecular models with Bentopy. Protein Science. 2026. e70480. https://doi.org/10.1002/pro.70480 This record contains the cell, mitochondrion, and aerosol models as described in the referenced article. For each model, the following files are provided. Input coordinate files for the individual structures that were packed and the membranes and other large molecules that were used to inform masks. Input configuration file (input.bent). Placement list and log produced by bentopy-pack. Final merged model and topology before solvation (top). For the aerosol, the virion envelope structure is not present in this record. This model was created at the Amaro lab (Dommer et al., 2023) and will be published in the future. Instructions on the installation and usage of bentopy can be found in the repository. References Dommer A, Casalino L, Kearns F, et al. #COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol. The International Journal of High Performance Computing Applications. 2022;37(1):28-44. doi:10.1177/10943420221128233