(a)Three cellPACK HIV models with Env fluorophores are superimposed over their corresponding simulated fluorescence images.(b)Samples from each of six the models are shown.(c)A direct comparison of cellPACK results to observed data identify ingredient parameter ranges that lead to specific emergent behaviors. provide the most detailed experimental view of this level with many successes in the localization of larger macromolecules (such as ribosomes) within whole cells1,2. However, an atomic resolution view of this intermediate scale, in spite of its utility in hypothesis generation, science communication, and simulation, remains sparsely modeled and visualized compared to larger and smaller scales of study35. No methods currently exist to observe the mesoscale in atomic-resolution detail, however, many sources of data may be used to synthesize a view of this level. For the past twenty years, we have taken a semi-quantitative approach to integrate these diverse data into a coherent model, creating artistic depictions of cellular environments (Fig. 1a) based ultrastructural data from light and electron microscopy, atomic structures from x-ray crystallography and NMR spectroscopy, and biochemical data on concentrations and interactions6,7. More recently, we and other groups8have developed computational approaches that automate the steps of this semi-quantitative approach to extend the results from 2D AK-1 paintings into 3D models that can be explored, animated, simulated, analyzed, and easily edited and updated. This process involves two conceptual steps: gathering of data to create a recipe(s) for the model, and use of this recipe to build a virtual model. == Figure 1. == cellPACK creates 3D models of the cellular mesoscale.(a)This hand-drawn painting of HIV shows three complex packing typesvolumetric, surface, and procedural (fibrous)that must interoperate in a mesoscale modeler.(b)autoPACK is a generalized packing algorithm that positions collections of objects (ingredients) into, onto, or outside of volumes to satisfy provided constraints. It operates multiple types of packing algorithms efficiently on a single unified model using an efficient global tracking grid.(c)cellPACK is a biological extension of autoPACK optimized to pack molecular structures and other data types into biological volumes. In this image cellPACK generates an editable FGF10 model of HIV by packing a from a recipe of molecular ingredients30into the ultrastructure of an HIV envelope surface. Since the field of structural biology is advancing so quickly, methods to automate the first step of the pipeline, the generation of a recipe based on AK-1 available data, are essential. This is a challenging goal given the heterogeneous nature of the data, but we have developed automated methods for several key steps. For example, we have developed tools to integrate bioinformatics data from sources like Stanfords WholeCellViz9and atomic structures from the Protein Data Bank. Since much of the data that our approaches use require manual curation, we have begun projects to implement these recipes in a way that allows community experts to update and improve the recipes across all scales of detail, to extrapolate predictions where reasonable, and to vote with confidence values for all contributing parameters and resulting assemblies. Given a molecular recipe, the construction of a quantitative 3D mesoscale model requires solving a non-trivial loose-packing problem. In biological systems, this includes packing soluble, membranous, and fibrous components with proper localizations and biologically AK-1 relevant interactions. Packing problems are a popular topic of study in mathematics, engineering and biology. The non-biological methods are typically limited to simple components AK-1 such as boxes and spheres10,11, or to providing one non-interacting packing-type solution at a time, such as surface packing, volumetric packing, or tree branching algorithms12,13, which can only contribute partial solutions towards recreating the organic complexity of a mesoscale model like HIV (Fig 1a,c). Other common nonbiological methods pack non-discrete components that can expand to fill space or contract to avoid overlaps14or rely on macroscale gravitational forces15,16. Physicists and engineers.