Patent ID: 6622094
Filing Date: 2003-09-16
Classification: C07K,G16B,G16C

Abstract:
A method for using a computer which processes data representing physical or energetic characteristics of a first molecule having a first chemical structure and a second molecule having a second chemical structure which is different from the first chemical structure, to determine a free energy difference between the first molecule and the second molecule, the method comprising:a) selecting a representation of the first molecule with a conformation characterized by a particular set of coordinates that define the position of each atom in the first molecule; b) determining the energy of the representation of the first molecule; c) assigning as starting coordinates the coordinates of the representation of the first molecule, transforming randomly the starting coordinates to a set of transformed coordinates, and assigning the transformed coordinates to be the coordinates of a representation of the second molecule to produce a particular conformation of the second molecule characterized by a particular set of coordinates that define the position of each atom in the second molecule; d) determining the energy of the representation of the second molecule; e) selecting either the representation of the first molecule or the representation of the second molecule to be added to an ensemble based on the relative energies of the representations of the first molecule and the second molecule, respectively; f) repeating a) through e) iteratively until a first molecule population in the ensemble and a second molecule population in the ensemble are stabilized; and g) determining the free energy difference between the first molecule and the second molecule by using the stable first molecule and second molecule populations in the ensemble.