Beyond AlphaFold - In Silico, Zero Shot Manipulation of Large Protein Complexes

Project Description

The core of all biological processes are protein-protein interactions, or PPI. PPI have distinctly complex and varied structural features. These complexities make novel material generation to probe and manipulate proteins difficult. The recent advent of open-source and AI design software permits de novo protein design at scale, reducing the need for extensive experimental optimization. However, almost all current AI design workflows lack the ability to generate de novo protein interactors within biological context, often limiting a target design space to <800 amino acids. This is due to a size limit imposed by GPU architecture on protein structure modeling software like AlphaFold. We developed a proprietary technology, Empyrean, which is a physics-based protein structure modeling approach with effectively no size limits. Furthermore, this software is low-compute, running on a single commercial CPU, to generate large, realistic structures in <20 minutes (validated up to 40,000 amino acids). Empyrean coupled with de novo design software will permit the generation of hundreds of thousands of design candidates within hours against any class of protein complex.

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