Clare E. West

Doctoral Student, University of Oxford

Clare

About

I am a second year DPhil student working on template-free protein structure prediction, under the supervision of Prof. Charlotte Deane and Saulo de Oliveira, in collaboration with Jiye Shi and Sebastian Kelm at UCB. I am a member of the Oxford Protein Informatics Group (OPIG), based at the Department of Statistics, University of Oxford.



Research

Protein structures can elucidate functional understanding, explain disease mechanisms and inform drug design. The aim of my research is to improve the computational prediction of long and multidomain protein structures, which are biologically crucial but particularly difficult to determine. These proteins have complex topologies and exploring the full conformational space is computationally intractable. In vitro, a subset of soluble proteins are able to correctly refold from a denatured state, but for many this is extremely difficult, inefficient or impossible. However, in living cells, directional elongation, non-uniform translation speeds, as well as spatial restrictions due to the ribosome and cellular crowding, all limit the conformational search space and may promote energetically favourable folding intermediates. Given the high efficiency of protein folding in vivo, we aim to include biologically-inspired methods in our protein structure prediction software. In turn, using computational methods to reveal interesting folding mechanisms may inform our understanding of biology.



Background

2015 - present DPhil Systems Approaches to Biomedical Science, University of Oxford (Lincoln College)
Exploring protein folding mechanisms to enable the protein structure prediction of previously intractable targets.
2016 Three month research project, Mathematical Institute, University of Oxford
Optimising anti-cancer treatment schedules to exploit competition and delay growth of therapy-resistant tumours, supervised by Prof. Helen Byrne and Prof. Eamonn Gaffney (Wolfson Centre for Mathematical Biology), Michael Davis and James Yates (AstraZeneca).
2012 - 2015 BSc (Hons) Biochemistry, University of Nottingham
Six month research project with Dr Ed Bolt, investigating the effect of a truncation mutation within the human DNA repair gene HELQ and its archaeal homologue Hel308.
2014 Ten week research placement, University of Nottingham
Working with Marios Georgiou, investigating cancer cell signalling and morphology using Drosophila as a model.
2014 One month work experience, Institute of Cancer Research
Working with the Oncogenetics team led by Prof. Ros Eeles, extracting DNA for Genome Wide Association Studies to identify genetic variants predisposing men to prostate cancer.

Contact


OPIG

Department of Statistics
University of Oxford
24-29 St Giles
Oxford OX1 3LB

Me

clare.west@stats.ox.ac.uk

Lincoln College
Oxford OX1 3DR

SABS DTC

Rex Richards Building
South Parks Road
Oxford OX1 3QU