Available student project - Protein structure: new topological methods

Research fields

  • Biophysics
  • Topological and Structural Science

Project details

We prefer to ignore the usual motifs of protein secondary and higher structure, and search for an alternative, robust measure of structure. One ("contact map") approach that we have developed involved measuring effective networks of graphs whose nodes are alpha carbons in the protein chain, and whose edges link nodes within a certain effective distance. This approach, for certain distances, allows sensitive detection of the interior and the surface of a protein. Can we use it to classify different proteins? 

A computational project is availabe that will explore the characterisitc length scales of our srtucutral probe for a suite of (hopefully many) proteins, analysing structural data from the Protein Data Bank (https://www.rcsb.org/) using our contact map technikque. 

Required background

Interest and curiosity in application of basic concepts of structure, protein folding and graph theory is essential. Familiarity with software coding, to automate analysis from a large database is preferred. 

Project suitability

This research project can be tailored to suit students of the following type(s)
  • PhB (2nd or 3rd year)
  • Honours project
  • Phd or Masters

Contact supervisor

Hyde, Stephen profile

Updated:  15 January 2019/ Responsible Officer:  Director, RSPE/ Page Contact:  Physics Webmaster