System and Method for Identifying Complex Patterns of Amino Acids

Abstract

A method and system are disclosed for identifying and/or locating complex patterns in an amino acid sequence stored in a computer file or database. According to an aspect of the present invention, techniques are provided to facilitate queries of protein databases. For protein descriptions received in response to the queries, embodiments of the present invention may scan the received protein descriptions to identify and locate Replikin patterns. A Replikin pattern is defined to be a sequence of 7 to about 50 amino acids that include the following three (3) characteristics, each of which may be recognized by an embodiment of the present invention: (1) the sequence has at least one lysine residue located six to ten amino acid residues from a second lysine residue; (2) the sequence has at least one histidine residue; and (3) at least 6% of the amino acids in the sequence are lysine residues.

1 - 10 . (canceled) 
     
     
         11 . A method of recognizing a scaffolding structure of amino acids, comprising:
 assembling a list of Replikin patterns occurring in a plurality of proteins; and   identifying the scaffolding structure as a pattern of substantially fixed amino acid residues occurring in each Replikin pattern in the list.   
     
     
         12 . The method of  claim 11 , wherein the plurality of proteins includes variants of the same protein. 
     
     
         13 . The method of  claim 11 , wherein the plurality of proteins includes different proteins. 
     
     
         14 . A method of forecasting onset of disease, comprising:
 determining a first count of Replikin patterns occurring in a protein at a first time;   determining a second count of Replikin patterns occurring in the protein at a second time; and   reporting an increased probability of future disease caused by an organism harboring the protein when the second count is greater than the first count.   
     
     
         15 . A method of synthesizing a vaccine, comprising:
 assembling a list of Replikin patterns occurring in variants of a protein associated with a disease-causing organism;   identifying a scaffolding structure of amino acids as a pattern of substantially fixed amino acid residues occurring in each Replikin pattern in the list;   selecting elements of the scaffolding structure, wherein said elements are conserved over time and wherein said elements are represented in a current variant of the protein; and   synthesizing a vaccine based on the selected elements.   
     
     
         16 . The method of  claim 15 , wherein the disease-causing organism is influenza.