Structural biology x topology
The future of structural biology requires new theoretical frameworks. It should someday be possible to create detailed models of entire cells and organisms with data-driven AI/ML. Therefore, we are making membranes tractable to informatics.
Category theory
Category theory is the skeleton of the proteolipid code. The entire membrane is a topological space on which we define a cover on called zonation. Zones include individual proteins and their imprint of lipids, clusters of protein and their collective lipid imprints, and voids that are devoid of protein. We can then use sheaf theory to assign to each zone some attributes; primary, secondary, tertiary, and quaternary, which are useful for discussing emergent properties such as in protein structure.
The gluing property of sheaves allows for the integration of data at increasingly higher scales, from zones to tissues, organs, and organisms. In essence, this is a categorical alternative to Karl Friston’s proposal (https://arxiv.org/abs/1906.10184).
Database
We want to create a database of zones and substructures such as protein-lipid and lipid-lipid interactions. To be updated.
Simulations
We are creating a lattice model as a proof-of-concept for more advanced simulations of life. To be updated.