Presented herein is a method for protein engineering that constructs a three-dimensional grid space around a protein. Different probes simulating amino acid interactions are placed within the grid. Pair Interaction Energy is calculated using the FMO technique for probe-protein interactions. An algorithmic process calculates the sum of PIEs, extending from each grid point to its neighbours, until a higher cumulative PIE is obtained. Grid points are then grouped into patches, and an alignment process matches a derived query probe pattern from each patch against the internal database’s existing patterns. Mutations are made based on the highest PIE probe-amino acid pairs from the matched pattern. This process can be iterated for generating optimal variants and can be localised to any part of the protein for the identification of patches. The invention covers a computer system and a non-transitory computer-readable medium to implement the disclosed method.
Patent No.: 567907
Date of grant: 26-06-2025