Patent ID: 9697305
Date: 2017-07-04
CPC Classifications: G06F,G16B

Claim:
1. A method of identifying a thermodynamic effect of an atomic replacement, insertion or deletion in a native polymer, the method comprising: at a computer system having one or more processors and memory storing one or more programs to be executed by the one of more processors: (A) using a derived set of three-dimensional coordinates for a derivation of the native polymer, wherein the derived set of three-dimensional coordinates that form the derivation of the native polymer comprises incorporation of an atomic replacement of one or more atoms that are in the native polymer, or an insertion or deletion a of one or more residues relative to the sequence of residues of the native polymer, to compute a first effective atomistic Hessian of a first portion of the derived set of three-dimensional coordinates that represents a first portion of the derivation of the native polymer, wherein each respective three-dimensional coordinate in the derived set of three-dimensional coordinates is a three dimensional coordinate for an atom in a first plurality of atoms in the derivation of the native polymer; (B) using a native set of three-dimensional coordinates for the native polymer to compute a second effective atomistic Hessian of a second portion of the native set of three-dimensional coordinates that represents a second portion of the native polymer, wherein each respective native three-dimensional coordinate in the native set of three-dimensional coordinates is a three dimensional coordinate for an atom in a second plurality of atoms in the native polymer; (C) computing a thermodynamic property of the first portion of the derivation of the native polymer using the derived set of three-dimensional coordinates and the first effective atomistic Hessian; and (D) computing a thermodynamic property of the second portion of the native polymer using the native set of three-dimensional coordinates and the second effective atomistic Hessian.