The Xplor-NIH_pcs comprises of modifications I have made to the Xplor-NIH distribution to allow full 8 parameter X-tensor determination.

pyParaTools 0.1 will be released in the next few weeks. Please check back regularly. The paper (proposed Bioinformatics application note) is in preparation.

I will be presenting a poster at ICMRBS in Cairns (22/08/10- 27/08/10). This poster will describe the core features of pyParaTools with an emphasis on using the program to solve interesting protein structure problems.

A paper that I have contributed to: "Tunable paramagnetic relaxation enhancements by [Gd(DPA)(3)] (3-) for protein structure analysis" has been published online.

Numbat was recently cited by a nice paper from Fuyuhiko Inagaki's group in Japan. Their paper is titled "PCS-based structure determination of protein–protein complexes". The authors use Numbat to determine the X-tensor's induced from a lanthanide tagged component in a hetero-dimeric complex. They subsequently solve the structure of the protein-protein complex.

Welcome to Mitchell Jon Stanton-Cook’s personal website - BmMG @ ANU


I am a PhD student in Dr Thomas Huber’s Biomolecular Modelling Group within the Research School of Chemistry (RSC) at the Australian National University (ANU). The members of my associate supervisory team are Dr Nicholas Hamilton and Dr Justine Hill. I collaborate closely with Professor Gottfried Otting and his Group at ANU. My PhD thesis is titled: “Computing protein interactions using NMR effects from paramagnetic labels”.

Research themes

Paramagnetic effects provide rich structural information in the form of long-range distance and, or, orientational information not available from conventional Nuclear Magnetic Resonance (NMR) measurements. When a paramagnetic metal ion, such characterised by unpaired electrons, is introduced into a protein, facilitated through the availability of a native binding site, or by exploiting readily available tagging agents, the pseudocontact shift (PCS), paramagnetic relaxation enhancement (PRE) and residual dipolar coupling (RDC) are features readily measured in NMR experiments . These effects are becoming frequently exploited in problems such as the assignment of spectra, the characterisation of molecular interactions, and in the detection and reconstruction of protein dynamics.


Figure 1. The changes in a NMR spectrum as the result of of a paramagnetic ion. Schematic illustration of the relationship between the position and, or, orientation of the paramagnetic ion (orange sphere) and nuclear active spin(s) (white sphere) probed by the new experimental observables.

The problems I am investigating are:

  • Paramagnetic NMR technique development (in a theoretical and applied manner)
  • The use of PCS in characterisation protein-ligand interactions in high resolution
  • The characterisation of the difference between the χ-tensor and the alignment-tensor
  • The study of protein dynamics and domain-motions using paramagnetic NMR effects
  • Solving the NMR homodimer problem with paramangentic NMR effects
  • Software development
  • Molecular dynamics simulation