Doctoral Student, University of Oxford
I am a second year DPhil student working on template-free protein structure prediction, under the supervision of Professor Charlotte Deane and Dr Saulo de Oliveira, 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 on Introduction to Programming and Structural Biology courses 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.
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.
|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.
|Clare E. West, Saulo H.P. de Oliveira, Eleanor C. Law, Sebastian Kelm, Jiye Shi, Charlotte M. Deane, Efficient Sampling for the Prediction of Long and Multidomain Protein Structures (Poster), Biophysical Society 62nd Annual Meeting (2018)|
|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.|
|Tutor for Biophysical Chemistry, Biochemistry Department, University of Oxford
A course for first-year Biochemistry undergraduates.
|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.