Patent Document ID: 7895024
Application ID: 11852671
Patent Flag: 1

Claim One:
1. An apparatus 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 apparatus comprising a suitably programmed computer, further comprising: a memory; and at least one processor coupled to the memory, and operative to: form three composite pattern descriptors from one-dimensional amino acid sequence patterns identified using pattern-discovery 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 that is known to form a π- helix, 3 10 - helix, or a kink in three dimensions, and wherein individual amino acids comprise classes and wherein amino acids within each class are permitted to replace each other within the same class; compare 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; use 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]; label 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-dimensional amino acid query sequence, wherein |x 1 |/√{square root over ((x 1 2 +x 2 2 +x 3 2 ))}, |x 2 |/√{square root over ((x 1 2 +x 2 2 +x 3 2 ))} and |x 3 |/√{square root over ((x 1 2 +x 2 2 +x 3 2 ))} are used to determine the label of each individual amino acid of the one-dimensional query sequence in a Π-helix, 3 10 -helix, or kink non-canonical category, and X 1 , x 2 and x 3 represent amounts assigned to each individual amino acid of the query sequence, and wherein: 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 1 |/√{square root over ((x 1 2 +x 2 2 +x 3 2 ))} is greater than or equal to 2.5 times |x 2 |/√{square root over ((x 1 2 +x 2 2 +x 3 2 ))} and greater than or equal to 2.5 times |x 3 |/√{square root over ((x 1 2 +x 2 2 +x 3 2 ))}; the individual amino acid of the one-dimensional query sequence would be labeled as belonging to a 3 10 -helix category if for the individual amino acid, |x 2 |/√{square root over ((x 1 2 +x 2 2 +x 3 2 ))} is greater than or equal to 2.5 times |x 1 |/√{square root over ((x 1 2 +x 2 2 +x 3 2 ))} and greater than or equal to 2.5 times |x 3 |/√{square root over ((x 1 2 +x 2 2 +x 3 2 ))}; 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 3 |/√{square root over ((x 1 2 +x 2 2 +x 3 2 ))} is greater than or equal to 2.5 times |x 1 |/√{square root over ((x 1 2 +x 2 2 +x 3 2 ))} and greater than or equal to 2.5 times |x 2 |/√{square root over ((x 1 2 +x 2 2 +x 3 2 ))}; the individual amino acid of the one-dimensional query sequence would be labeled as a hybrid between a π-helix category and a 3 10 -helix category if for the individual amino acid, |x 1 |/√{square root over ((x 1 2 +x 2 2 +x 3 2 ))} is greater than or equal to 2.5 times |x 3 |/√{square root over ((x 1 2 +x 2 2 +x 3 2 ))} and |x 2 |/√{square root over ((x 1 2 +x 2 2 +x 3 2 ))} is greater than or equal to 2.5 times |x 2 |/√{square root over ((x 1 2 +x 2 2 +x 3 2 ))}; 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 1 |/√{square root over ((x 1 2 +x 2 2 +x 3 2 ))} is greater than or equal to 2.5 times |x 2 |/√{square root over ((x 1 2 +x 2 2 +x 3 2 ))} and |x 3 |/√{square root over ((x 1 2 +x 2 2 +x 3 2 ))} is greater than or equal to 2.5 times |x 2 |/√{square root over ((x 1 2 +x 2 2 +x 3 2 ))}; the individual amino acid of the one-dimensional query sequence would be labeled as a hybrid between a 3 10 -helix category and a kink category if for the individual amino acid, |x 2 |/{square root over ((x 1 2 +x 2 2 +x 3 2 ))} is greater than or equal to 2.5 times |x 1 |/√{square root over ((x 1 2 +x 2 2 +x 3 2 ))} and |x 3 |/√{square root over ((x 1 2 +x 2 2 +x 3 2 ))} is greater than or equal to 2.5 times |x 1 |/√{square root over ((x 1 2 +x 2 2 +x 3 2 ))}; and the individual amino acid of the one-dimensional query sequence would be otherwise labeled as a hybrid between all three non-canonical categories; and output said determination to a user.