Patent Document ID: 20080171904
Application ID: 11852691
Patent Flag: 0

Claim One:
1. An article of manufacture for determining whether an amino acid in a one-dimensional amino acid query sequence belongs to one of three non-canonical helical conformations, wherein the three non-canonical helical conformations are π-helices, 3 10 -helices, and kinks, wherein the kinks comprise proline-induced kinks and non proline-induced kinks, comprising a machine readable medium containing one or more programs which when executed implement the steps of: forming three composite pattern descriptors from one-dimensional amino acid sequence patterns identified using pattern-discovery means by processing instances of one-dimensional amino acid sequences that are known to form non-canonical helical conformations belonging to each of π-helices, 3 10 -helices, and kinks, respectively, wherein each instance is a one-dimensional amino acid sequence fragment, and wherein individual amino acids comprise classes and wherein amino acids within each class are permitted to replace each other within the same class; comparing each composite pattern descriptor with the one-dimensional amino acid query sequence to determine whether one or more amino acid sequence patterns that form the three composite pattern descriptors have an instance in the one-dimensional amino acid query sequence; using said instances to determine whether a given amino acid in the one-dimensional amino acid query sequence belongs to one of the three non-canonical helical conformations, wherein the three non-canonical helical conformations are π-helices, 3 10 -helices, and kinks, and wherein the determination indicates one or more local three-dimensional structures within a protein; and outputting said determination to a user.