Patent ID: 7167851

Claim:
A computer-implemented method of predicting functional similarity between two molecules comprising: deriving a first one-dimensional representation of a first molecule with a known chemical behavior from distances between selected atoms of said first molecule, said one dimensional representation comprising a string of atoms, each atom of said string having a selected type, a selected width, and a selected position along said string; deriving a second one-dimensional representation of a second molecule with an unknown chemical behavior from distances between selected atoms of said second molecule, said one dimensional representation comprising a string of atoms, each atom of said string having a selected type, a selected width, and a selected position along said string; and comparing said one dimensional representations, wherein the comparing comprises: aligning the one dimensional representations such that the position of an atom of a first selected type in the first one dimensional representation coincides with the position of an atom of the first selected type in the second one-dimensional representation; and evaluating the amount of overlap between atoms of each selected type in the first one-dimensional representation and atoms of the same type in the second one-dimensional representation; and identifying the second molecule as likely to have similar chemical behavior as the first molecule based on said comparing.