Patent ID: 7672788
Filing Date: 2010-03-02
Classification: G16B

Abstract:
1. A method for determining N disulphide bond connections in a protein comprising 2N bonded sulphur atoms, each sulphur atom being available for forming the N disulphide bond connections through use of an undirected graph having the 2N sulphur atoms as nodes and having an edge connecting each pair of nodes of the N nodes, each edge being a potential disulphide bond connection of the N disulphide bond connections to be determined, each sulphur atom of the 2N sulphur atoms being independently comprised by a cysteine of the protein, said cysteines being sequenced along a chain in the protein in accordance with an ordered list of position indexes 0, 1, 2, . . . , said N at least 2, said method comprising: determining an edge weight W for each edge between a first sulphur atom S a processor of a computer system determining the N disulphide bond connections by optimizing an objective function formed from the determined edge weights W, wherein the objective function is a sum of the weights of the N disulphide bond connections, and wherein said optimizing comprises determining the N disulphide bond connections that maximize the objective function, and transmitting to an output device an identification of the determined N disulphide bond connections, wherein said determining the edge weights comprises: wherein a and b are positive real numbers subject to a/b being in a range of 1.0 to 1.5, wherein W wherein the function W wherein for each edge at which said calculating the edge weight W is according to W=aW wherein Σ wherein the at least one penalty is selected from the group consisting of a proximity penalty, a bending penalty, and both the proximity penalty and the bending penalty, wherein the proximity penalty applies if |I wherein the bending penalty applies if a minimum distance between S