Nicholas Pearce

DPhil Student, Systems Approaches to Biomedical Sciences (SABS), Oxford University.

Based in the Structural Genomics Consortium, The Department of Statistics, and the Doctoral Training Centre.



Structural Genomics Consortium,
Old Road Campus Research Building,
Roosevelt Drive,
Oxford, OX3 7DQ



Department of Statistics,
The Peter Medawar Building,
South Parks Road,
Oxford, OX1 3SY



Doctoral Training Centre,
Rex Richards Building,
South Parks Road,
Oxford, OX1 3QU.


About Me


Current Research

I am currently a 4th Year DPhil Student on the Systems Approaches to Biomedical Sciences programme (SABS) at Oxford University. I am primarily based at the Structural Genomics Consortium (SGC), but I also spend time in the Statistics Department.

My DPhil research primarily centres around interpreting electron densities from fragment soaking datasets. These screening experiments generate a wealth of structural data, and we wish to extract as much information about the binding of fragments to the protein binding site as possible.

Background

  • MPhys in Physics from Oxford University
    Major Options:
      • Theoretical Physics
      • Condensed Matter Physics

Awards

  • Undergraduate Scholar of Worcester College, Oxford
  • NTT Prize for an MPhys Project in Biological Physics

Undergraduate Research

  • MPhys Project - Translocation of Biopolymers.
    Rudolf Peierls Centre for Theoretical Physics, Oxford University
  • Summer Project - Propogation of Spin Waves on a 2D Antiferromagnetic Lattice.
    Rudolf Peierls Centre for Theoretical Physics, Oxford University

Graduate Research

For the first year of the DPhil, I was based at the Doctoral Training Centre taking various courses related Systems Biology. These spanned Statistics, Structural Biology, Molecular Genetics, Mathematical Biology, Theoretical Biology, Organic Chemistry and other fields. I also undertook two short 10 week projects:

1st Project

The first of the short projects was focussed on modelling the variable domains of antibodies (without the CDRs) to high resolution. Since the domains of antibodies are highly structurally conserved, we should be able to model them to high accuracy (within 1 angstrom rmsd). We adapted the protocol used by MEDELLER to model the domains, with some success.

2nd Project

The second of the short projects was targeted towards the development of a scoring system for rapidly assessing the agreement of a residue to electron density. A training set of partially complete protein models was generated, with the gaps filled with a number of loop models built by FREAD. The residues in these loops were scored against the electron density from the diffraction experiments. By comparing the residues in the loops to the corresponding residues in the PDB structure (the `correct' structure) we could train a scoring system that will determine, rapidly, the quality of residues in a model.

Short Biography

I'm a 4th Year DPhil student on the Systems Approaches to Biomedical Sciences (Industrial Doctoral Centre - IDC) Programme at Oxford University.

Originally trained in Physics, I have completed the first year of the IDC and am now starting my DPhil research. I am a student based in the Nuffield Department of Medicine at the Structural Genomics Consortium (SGC), but I am also associated with the department of Statistics.

Contact Me

If you have any questions about my research, please feel free to contact me.

E-mail: nicholas.pearce@dtc.ox.ac.uk