US 2010/0138205 A1 · STOCHASTIC MOLECULAR BINDING SIMULATION

Abstract

The invention provides methods of dynamically simulating molecular interactions between a target molecule and a plurality of ligand molecules. The ligand molecules may be presented in the model as a homogeneous set of identical ligands or as a heterogeneous set of different ligands, such as, for example, a set of structural variants of a ligand molecule. Typically, the ligand molecule will be a small organic compound, such as a drug or other small molecule, and the ligand will be a protein or a protein domain, a nucleic acid (i.e., DNA, RNA), or a biomolecular complex of proteins and/or nucleic acid molecules. Unlike all known molecular dynamics simulation methods, the invention provides ligand molecules to the simulation's interaction environment(s) in excess relative to the target molecule.

Claims18

Dependent claims

A method of simulating the interaction between a ligand and a target molecule, comprising:

a. providing a computer-generated interaction environment having volumetric dimensions as large or larger than the known or predicted maximum volume of the target molecule;
b. populating the interaction environment with the three-dimensional structure of a single target molecule and a plurality of ligand molecules, wherein the ligand molecules are positioned at least three times the estimated diameter of the ligand molecule from the target molecule;
and,
c. conducting a molecular dynamics simulation, in which the free energy includes entropy, and observing the interaction dynamics between one or more ligand molecules and the target molecule.

1 more element

Dependencies are inferred from the claim text.

Stochastic molecular binding simulation

Life of this patent

Stochastic molecular binding simulation

Life of this patent

Abstract

Claims18