METHODS AND SYSTEMS FOR ALCHEMICAL BINDING FREE ENERGY CALCULATIONS

Abstract: a computer-implemented method can include: obtaining a plurality of chemical compounds each having an initial condition and a final condition; computing comparative distances of areas of each of the plurality of chemical compounds in the initial condition and in the final condition, wherein the distances are calculated based on a physical configuration and electrical potential of each chemical compound; forming one or more clusters of the plurality of chemical compounds based on the computed comparative distances of the areas of each of the plurality of chemical compounds; and generating a diagram of changes for the plurality of chemical compounds, the diagram including a plurality of nodes and a plurality of edges, wherein each node indicates one chemical compound, and each edge is a transition from one chemical compound to another chemical compound of the plurality of chemical compounds; sampling conformational states of chemical compounds, preserving reliable microstates and ensuring an optimal transition pathway along with reproducible free energy estimates.

Inventor(s): Vladimir Aleksandrovich Aladinskiy, Georgy Andreev, Evgeny Kirilin, Aleksandrs Zavoronkovs

CPC Classification: G16C20/50 (Molecular design, e.g. of drugs)

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