Modeling in the Time of COVID-19: Statistical and Rule-based Mesoscale Models

We present a new technique for rapid modeling and construction of scientifically accurate mesoscale biological models. Resulting 3D models are based on few 2D microscopy scans and the latest knowledge about the biological entity represented as a set of geometric relationships. 
Our new technique is based on statistical and rule-based modeling approaches that are rapid to author, fast to construct, and easy to revise. From a few 2D microscopy scans, we learn statistical properties of various structural aspects, such as the outer membrane shape, spatial properties and distribution characteristics of the macromolecular elements on the membrane. This information is utilized in 3D model construction. Once all imaging evidence is incorporated in the model, additional information can be incorporated by interactively defining rules that spatially characterize the rest of the biological entity, such as mutual interactions among macromolecules, their distances and orientations to other structures. These rules are defined through an intuitive 3D interactive visualization and modeling feedback loop.
We demonstrate the utility of our approach on a use case of the modeling procedure of the SARS-CoV-2 virus particle ultrastructure. Its first complete atomistic model, which we present here, can steer biological research to new promising directions in fighting spread of the virus.
KAUST CEMSE NANOVIS Resources SARS COV 2 Outer Structure
Outer structure of the SARS-COV-2 showing membrane bound proteins.
KAUST CEMSE NANOVIS Resources SARS COV 2 Inner Structure
Inner structure of N protein rope that is scaffolding the viral RNA.


N. Nguyen, O. Strnad, T. Klein, D. Luo, R. Alharbi, P. Wonka, M. Maritan, P. Mindek, L. Autin, D. Goodsell, I. Viola: Modeling in the Time of COVID-19: Statistical and Rule-based Mesoscale Models‌, arXiv preprint,, 2020


Download the model from KAUST repository CC

The model has been built in tight cooperation with Scripps Research and the rendering has been done in real-time by Nanographics.

Making of SARS-CoV-2 mesoscale model
Literature Review - Towards the atomistic model of RNP core for SARS-CoV-2