Clare E. West

Doctoral Student, University of Oxford

About Research Background Publications Teaching Contact
Clare

About

I am a fourth year DPhil student working on template-free protein structure prediction, under the supervision of Professor Charlotte Deane and Dr Saulo de Oliveira (Stanford University), in collaboration with Jiye Shi and Sebastian Kelm at UCB Pharma. I am a member of the Oxford Protein Informatics Group (OPIG), based at the Department of Statistics, University of Oxford. I tutor Biochemistry undergraduates in Biophysical Chemistry, as well as demonstrating for courses in Programming and Structural Biology at the Doctoral Training Centre. In my roles as Website Officer for the science outreach society Oxford Hands-on Science (OxHOS), and graduate student representative on the Department of Statistics' Good Practice Steering Group, I pursue my interest in widening access and inclusion in science.

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

Clare
DPhil Systems Approaches to Biomedical Science, University of Oxford (Lincoln College)
2015 - present

Exploring protein folding mechanisms to enable the protein structure prediction of previously intractable targets.
POST Fellowship, Parliamentary Office of Science and Technology
September 2018 - January 2019

Produced a POSTnote (Parliamentary briefing) on the Cyber Security of Consumer Devices.
Three month research project, Mathematical Institute, University of Oxford
2016

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).
BSc (Hons) Biochemistry, University of Nottingham
2012 - 2015

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.
Ten week research placement, University of Nottingham
2014

Working with Marios Georgiou, investigating cancer cell signalling and morphology using Drosophila as a model.
One month work experience, Institute of Cancer Research
2014

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.

Publications and Presentations

Clare E. West, Saulo H.P. de Oliveira & Charlotte M. Deane. (2019) RFQAmodel: Random Forest Quality Assessment to identify a predicted protein structure in the correct fold (preprint). BioRxiv.
Clare E. West & Lydia Harriss. (2019) Cyber Security of Consumer Devices (Parliamentary Briefing), POSTnote 593, Parliamentary Office of Science and Technology
Clare E. West, Saulo H.P. de Oliveira, Eleanor C. Law, Sebastian Kelm, Jiye Shi, Charlotte M. Deane. (2018) Efficient Sampling for the Prediction of Long and Multidomain Protein Structures (Poster), Biophysical Society 62nd Annual Meeting
Bernhard Knapp, Marta Alcala, Hao Zhang, Clare E. West, P Anton van der Merwe, Charlotte M Deane. (2018) pyHVis3D: Visualising Molecular Simulation deduced H-bond networks in 3D: Application to T-cell receptor interactions. Bioinformatics.



Teaching

Tutor for Biophysical Chemistry, Biochemistry Department, University of Oxford
A course for first-year Biochemistry undergraduates, including Quantum Mechanics, Basic Thermodynamics, Chemical Kinetics and Spectroscopy.
Demonstrator, Doctoral Training Centre, University of Oxford
Introduction to Programming and Structural Biology modules, which are intensive two-week courses to introduce interdisciplinary students to unfamiliar fields.

Contact


OPIG

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

Me

clare.west@stats.ox.ac.uk

SABS DTC

Rex Richards Building
South Parks Road
Oxford OX1 3QU