System and method for using physics-based depictions of protein shapes in visualization and shape-conditioned drug candidate generation

A computing system, comprising:

• one or more processors;
• and
• a memory storing instructions that, when executed by the one or more processors, cause the system to perform operations comprising:
• selecting a plurality of regions on a molecule, each region comprising a plurality of atoms;
• within each of the plurality of regions, computing nonbonded interactions between each pair of the plurality of atoms in the region to obtain a plurality of physical attributes of the region, each of the plurality of physical attributes representing an interaction strength between the pair of atoms;
• constructing a point cloud for each of the plurality of regions based on the plurality of physical attributes of the region;
• obtaining a drug candidate for bonding to a target region in the plurality of regions;
• and
• performing molecule modification on the drug candidate to match a shape of the point cloud of the target region.

A non-transitory computer-readable storage medium configured with instructions executable by one or more processors to cause the one or more processors to perform operations comprising:

• selecting a plurality of regions on a molecule, each region comprising a plurality of atoms;
• within each of the plurality of regions, computing nonbonded interactions between each pair of the plurality of atoms in the region to obtain a plurality of physical attributes of the region, each of the plurality of physical attributes representing an interaction strength between the pair of atoms;
• constructing a point cloud for each of the plurality of regions based on the plurality of physical attributes of the region;
• obtaining a drug candidate for bonding to a target region in the plurality of regions;
• and
• performing molecule modification on the drug candidate to match a shape of the point cloud of the target region.