A method, computer system, and computer program product for determining N disulphide bond connections in a protein having 2N bonded sulphur atoms. Each sulphur atom is 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. Each sulphur atom is comprised by a cysteine of the protein. The cysteines are sequenced along a chain in the protein as ordered list of position indexes. A weight W of each edge between cysteine position indexes I1 and I2 is calculated as decreasing with increasing separation d between I1 and I2, wherein d is |I1−I2|/100. The N disulphide bond connections are determined by optimizing an objective function formed from the calculated weights W.