IDENTIFICATION OF BINDING SITES IN A PROTEIN STRUCTURE

Organization Name

Inventor(s)

Benjamin Thomas Walters of South San Francisco CA (US)

IDENTIFICATION OF BINDING SITES IN A PROTEIN STRUCTURE

This abstract first appeared for US patent application 18960282 titled 'IDENTIFICATION OF BINDING SITES IN A PROTEIN STRUCTURE

Original Abstract Submitted

In one aspect, a method for identifying residues in a particular conformation of a protein molecule capable of forming a stable binding between a compound and the protein molecule is provided. The method can include identifying, for inclusion in a perturbation set, one or more residues from the conformation of the protein molecule that exhibit a protection factor satisfying one or more thresholds. One or more residues may be excluded from the perturbation set based at least on a spatial arrangement and/or an orientation of the one or more residues. One or more rounds of molecular dynamics simulations whose result is indicative of an interaction between the compound and the residues in the perturbation set may be performed. The residues in the perturbation set may be identified as forming a stable binding between the compound and the protein molecule based at least on the result of the molecular dynamics simulation