structural biology teams

Abstract: Biological models bring the molecular world of cells into view, enabling experts and the public to explore and understand biological discoveries. Building mesoscale models requires organizing many molecular components into spatial arrangements that can be revised as evidence and interpretations develop. We present MesoCraft, a browser-based tool for structural biologists centered on interactive procedural modeling. User-defined rules generate collections of molecular instances, while a geometry-node editor and visual feedback support authoring and revision of their spatial relationships. Beyond model construction, MesoCraft integrates exploration and communication, enabling researchers to inspect molecular organization and create guided animations that highlight key spatial relationships. By connecting modeling, exploration, and explanation in a unified workflow, MesoCraft allows insights gained during exploration and communication to inform iterative model refinement, supporting the development of mesoscale models into visual narratives of cellular organization. A demonstrative deployment of the tool is available at https://mesocraft.kaust.edu.sa/.

Abstract: CryoEM map interpretation requires features that are spatially localized, consistent across samples, and informative across spatial scales. Most deep learning methods for map annotation extract features from fixed voxel grids. However, implicit neural representations (INRs) are able to model volumetric data as scale-agnostic, coordinate-conditioned functions. INRs are therefore attractive for cryoEM, but fitting a separate INR for each map is too expensive for large-scale feature extraction and produces representations that are not aligned across samples. We introduce Atelier, a self-supervised framework that amortizes INR fitting for reconstructed cryoEM maps. Pretrained on 5,439 Electron Microscopy Data Bank maps, Atelier is a transformer-based hypernetwork that generates high-fidelity reconstructions across a wide range of protein structures, including large multi-subunit assemblies. Beyond reconstruction, the INR generated by the pretrained transformer exposes a continuous, local feature field through its intermediate activations at any spatial query point, a property that voxel grid and patch-tokenizer architectures do not naturally provide. Used as auxiliary channels to a 3D nested U-Net annotation head trained from scratch, these coordinate-conditioned features improve performance on eight voxel-level property prediction tasks over a volume-only baseline. Our results demonstrate that amortized implicit neural representations are an effective primitive for geometry-aware analysis of cryoEM data.