Patent ID: 7698067
Filing Date: 2010-04-13
Classification: G16B

Abstract:
1. A computer-implemented method 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, comprising the following steps: providing a system, wherein the system comprises a suitably programmed computer comprising distinct software modules, each of the distinct software modules being embodied on a tangible computer-readable recordable storage medium, and wherein the distinct software modules comprise a composite descriptor module, and an amino acid query sequence processing module, and wherein the system executes the following steps via the suitably programmed computer; 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 seciuence 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, wherein comparing each composite pattern descriptor with the one-dimensional amino acid query sequence is carried out by the amino acid query sequence processing module executing on a hardware processor; 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, wherein 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 is carried out by the amino acid query sequence processing module executing on a hardware processor; labeling 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 seciuence that contains the one-dimensional amino acid query sequence, wherein labeling the identified positions of the one-dimensional amino acid query sequence is carried out by the amino acid query sequence processing module executing on a hardware processor, wherein |x outputting said determination to a user, wherein outputting said determination to a user is carried out by the amino acid query sequence processing module executing on a hardware processor.