Patent ID: 7219020

Claim:
A method for calculating the similarity of at least one chemical compound to at least one chemical probe, comprising the steps of: (a) utilizing at least one chemical descriptor for each of a plurality of compounds, each descriptor comprising a row of a molecule-descriptor matrix X; (b) representing each compound as a column of the molecule-descriptor matrix, the entries of the molecule-descriptor matrix comprising a frequency of each descriptor for each compound; (c) performing a partial singular value decomposition (SVD) of the molecule-descriptor matrix to produce resultant matrices P, Σ, and Q T , comprising: generating the resultant matrices P, Σ, and Q T , such that molecule-descriptor matrix X=PΣQ T , wherein: P is a mxr matrix, called the left singular matrix, where r is the rank of X, and its columns are eigenvectors of XX T corresponding to nonzero eigenvalues: Q is a nxr matrix, called the right singular matrix, whose columns are eigenvectors of X T X corresponding to the nonzero eigenvalues; and Σ is a rxr diagonal matrix whose nonzero elements, σ 1 , σ 2 , . . . , σ r called singular values, are the square roots of the nonzero eigenvalues and have the property that σ 1 ≧σ 2 ≧ . . . ≧σ r ; (d) creating a chemical probe descriptor matrix for the at least one chemical probe, the entries of the chemical probe descriptor matrix comprising a frequency of each descriptor for each chemical probe; (e) calculating the similarity between the at least one chemical probe and at least one compound of the molecule descriptor matrix by: generating a reduced dimension approximation of X of rank k, defined as X k =P k Σ k Q T k , wherein k<r and Σ k is an identity matrix; generating a pseudo-object, denoted as O F , where O F =F T P k Σ −1 k , and where F is a molecule-descriptor vector for the at least one chemical probe; and taking a dot product of O F with one or more columns of O T k respectively corresponding to the at least one compound; and (f) providing an output indicating the similarity between the at least one chemical probe and the at least one compound.