Patent ID: 7991563
Filing Date: 2011-08-02
Classification: G16B

Abstract:
1. An article of manufacture for determining whether a one-dimensional amino acid query sequence encodes an instance of one of three types of deviations from α-helicity, wherein the three types of deviations from α-helicity comprise 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, the article of manufacture comprising a tangible computer readable recordable storage medium comprising executable instructions for: 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 comparing each composite pattern descriptor with the one-dimensional amino acid query sequence, wherein the query sequence is derived directly from a fragment of rhodopsin, wherein the fragment of rhodopsin comprises a contiguous sequence of amino acids derived directly from rhodopsin, 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 the one-dimensional amino acid query sequence encodes an instance of one of the three types of deviations from α-helicity labeling the identified positions of the one-dimensional amino acid query sequence as forming a particular non-canonical protein structure, wherein the particular non-canonical protein structure will be formed by the amino acid sequence that contains the one-dimensionalamino acid query sequence, wherein |x the individual amino acid of the one-dimensional query sequence would be labeled as belonging to a π-helix category if for the individual amino acid, |x the individual amino acid of the one-dimensional query sequence would be labeled as belonging to a 3 the individual amino acid of the one-dimensional query sequence would be labeled as belonging to a kink category if for the individual amino acid, |x the individual amino acid of the one-dimensional query sequence would be labeled as a hybrid between a π-helix category and a 3 the individual amino acid of the one-dimensional query sequence would be labeled as a hybrid between a π-helix category and a kink category if for the individual amino acid, |x the individual amino acid of the one-dimensional query sequence would be labeled as a hybrid between a 3 the individual amino acid of the one-dimensional query sequence would be otherwise labeled as a hybrid between all three non-canonical categories; and outputting said determination to a user.