LSFG is a novel method for engineering proteins by utilizing an atomistic grid-based computational method that analyzes and compares protein atomic compositions. By arranging a protein’s atoms into a fine 3D grid, this approach captures atomic-level details in highly localized regions, allowing comparison of specific protein regions even in the absence of structural similarity. Unlike...
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...
The functional repurposing of structural proteins offers exciting opportunities for sustainable and efficient biocatalysis. This study presents the engineering of two structural proteins, F-actin, to exhibit nitrilase activity, enabling the conversion of 1-(cyanomethyl)cyclohexane-1-carbonitrile into 2-(1-cyanocyclohexyl)acetic acid, a key intermediate in the production of gabapentin. By introducing catalytic residues adapted from nitrilase enzymes, these engineered proteins...
The present invention describes identifying if a given Transaminase is (R)-Selective or (S)-Selective. Based on the binding of the substrate in the active site of a given transaminase, it is primarily based on torsion, the angle between specific atoms of the cofactor PLP and the catalytic Lysine, and the ten interactions of the substrate with...
The invention describes the methods of directing CRISPR complex formation in bacterial cells and utilizing the CRISPR-Cas system to edit a gene of interest in a plasmid. An AI incorporated CRISPR tool to engineer enzymes for better activity and allow cells to undergo specific and random mutation for a variety of research or translational applications,...
The invention is specific to the engineering of enzymes. The Michaelis Complex of E-S reaction is simulated using QM/MM, and MD methods. Using the QM polarized grid maps, MMPBSA. MMGBSA, low energy ES conformations that lead to the formation of attack conformation are identified. Subsequently, the enzyme is designed around the Michaelis complex where the...
The patented technology works on Quantum mechanics-based probes/grid points, and real solvation using semi-empirical QM simulations. The dynamic probes atoms in the grid are replaced based on the neighbor-neighbor contacts in the conformational transitions. The Dynamic grid points capture high-resolution details of the enzymatic reaction. The method was implemented on an R-specific transaminase enzyme and...
Kcat Enzymatic brings Enzyme Engineering & Biocatalysis Revolution by using upfront in-silico in-house developed methods and algorithms using 7D Grid Technology for enzyme engineering (Patent No: 201841047021). In this line, a new and advanced way of enzyme engineering methods were developed to use enzymes in industrial processes. Our multiscale methods and technologies gives custom engineered...
7D Grid Technology uses Quantum Mechanic probes to “capture information across the enzymatic reaction and across the enzyme-substrate system”. This information is used by AI methods, Convolutional Neural Networks, and Support Vector Machines, to design enzymes and derive focused libraries. Based on the projects done in the last 2.5 years, we can say that promiscuous...
