Patent ID: 6772073
Filing Date: 2004-08-03
Classification: C07K,G16B

Abstract:
A computer-assisted method for predicting the binding affinity of a compound for a binding target of a molecule, using a programmed computer including a processor, an input device, and an output device, including the steps of:i) inputting into the programmed computer, through the input device, data including the identity and three-dimensional coordinates of each of the atoms in the molecule; ii) determining, using the processor, for each atom in the molecule, a predicted Gibbs free energy of binding of the atom to an ideal ligand; iii) generating, using the processor, a three-dimensional prediction model of binding targets in the molecule by generating, using the three-dimensional coordinates of each of the atoms in the molecule, a model of the atoms in the molecule and mapping onto each atom depicted in the model the corresponding determined predicted Gibbs free energy of binding; iv) identifying as a binding target a region of the molecule with a high density of atoms which exhibit favorable Gibbs free energy of binding to said ideal ligand, v) inputting into the programmed computer, through the input device, data including the identity and three-dimensional coordinates of each of the atoms in the binding target, vi) inputting into the programmed computer, through the input device, data including the identity and three-dimensional coordinates of each of the atoms in the compound; vii) generating, using the processor, model of the compound bound to the binding target; viii) determining, using the processor, the three-dimensional coordinates of an energy minimized structure of the compound when the compound is bound to the binding target; and ix) determining, using the processor, a predicted binding affinity of the energy minimized compound for the binding target.