Patent ID: 7110888

Claim:
A method of constructing a representation of a set of molecules stored in a computer database for facilitating searching thereof, comprising: choosing an initial set of N molecules wherein N is less than a total number of molecules in the set of molecules and N is at least 2, and specifying a property of the set of molecules; calculating a distance matrix D wherein each element D ij is a minimal metric distance between said property of a molecule i and said property of a molecule j and wherein said molecule i and said molecule j are in said initial set of molecules; constructing a metric matrix G from D according to distance geometry; diagonalizing G, thereby obtaining eigenvalues of G, and obtaining a set of positions in N1-dimensional space that reproduce the distances in said matrix D to within a tolerance T, wherein each position of said set of positions has N-1 coordinates associated with it; determining for every molecule which of the N−1 coordinates that represent positions in a shape space of each of the N molecules can be eliminated such that a remaining number, M, of the N−1 coordinates still enables said distance matrix to be reproduced to within said tolerance, T; defining a shape space to be an M dimensional subspace occupied by the N molecules, such that said M-dimensional subspace is formed from M+1 molecules; and storing the shape space, thereby providing a representation that facilitates searching said set of molecules.