Patent ID: 7672791

Claim:
A computer-implemented method of identifying at least a portion of a molecule indexed in a database, the molecule having both a conformation and at least one physico-chemical property similar to those of a query molecule, the database including at least one conformation representation for each of a plurality of indexed molecules, wherein each of the indexed molecules is partitioned into a set of overlapping fragments, and in which at least one conformation representation is associated with each fragment, and in which for each of the fragment conformation representations, at least 3 computed features of interest of the fragment have been provided, each of said at least 3 computed features corresponding to a different, single point in 3-D physical space and representing at least one given physico-chemical property, the method comprising: a) providing a conformation of a query molecule that includes at least 3 computed features, each of which corresponding to a different, single point in 3-D physical space and corresponds to at least one physico-chemical property of interest, wherein at least one of the computed features of the query molecule is not located at an atomic site; b) using a computer for pattern matching said at least 3 computed features of the query molecule with corresponding computed features of fragments given by fragment conformation representations in the database to identify fragments having patterns of computed features similar to patterns of computed features in portions of the query molecule, wherein said pattern matching includes i) first matching just feature type and ii) then matching feature geometry; c) using a computer for assembling geometrically compatible overlapping fragment conformations corresponding to fragments identified by said pattern matching into at least one three-dimensional molecular structure that corresponds to at least a portion of at least one of the indexed molecules, in order to identify at least a portion of a molecule in the database having patterns of computed features similar to patterns of computed features in the query molecule; and d) using a computer to present, to a user, results generated by steps a), b), and c), so that the user is able to view and analyze the results.