Supervisor: Prof. Peter J. Artymiuk & Prof. Peter Willett

School: Bioinformatics and Chemoinformatics research group, University of Sheffield.

One function of proteins, the workhorses of cells, is to decode the genetic information stored within the nucleic acid material.  The way in which a specific protein molecule correctly recognises and interacts with its target nucleotide sequence from amongst the billions of nucleotide bases contained within a cell, is clearly of great interest. Increased knowledge of how these two types of molecules interact with one another can be applied as screens in docking experiments and rational drug design programs.

Here a program based on graph theory is used to carry out substructure searches within complexes of proteins and nucleic acids. Initial search patterns involve a pseudoatom representing an amino acid placed in six positions around a base pair, three in the major groove and three in the minor groove. Additional features of the program, called Nassamj, include a planarity measure to explore how planar an amino acid is to a base pair, actual hydrogen bonds formed based on distance and angle criteria, and a measure of which atoms are making real van der Waals contacts.

The results that have been obtained so far demonstrate that Nassamj can effectively locate substructures from within large structural complexes, and that there may be some correlation between the position and the nature of the interaction formed.