Research

My research field is Structural Bioinformatics, which means that I use computational methods to study the three-dimensional conformations of proteins. In particular, my work focusses on loops, which are the regions of a protein that are not part of secondary structure elements. Loops often play a key role in protein function; understanding their properties and knowing their structures is therefore extremely valuable.

I have developed a novel algorithm for the prediction of protein loop structures, called Sphinx. Sphinx uses a combination of knowledge-based and ab initio approaches to maximise our use of the available structural data. While it was originally designed to improve our ability to model the CDR H3 loops of antibodies, I have also developed versions for membrane protein loops and loops from non-specific protein types. I am also exploring ways to improve the prediction of long loops, through the inclusion of properties that can be predicted from sequence.

More recently, I have carried out analyses of loops which are able to adopt multiple conformations, and investigated the ability of several algorithms to predict their structures. Unfortunately, it seems that current methodologies are accurate for loops of a single conformation, but fail when they attempt to model conformational ensembles. For more information on this, or my other research, see my Publications list!

Publications

  1. C Marks, J Shi, C M Deane - Predicting loop conformational ensembles, Bioinformatics, 2017 [link]
  2. C Marks, J Nowak, S Klostermann, G Georges, J Dunbar, J Shi, S Kelm, C M Deane - Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction, Bioinformatics, 2017 [link]
  3. C Marks, C M Deane - Antibody H3 Structure Prediction, Computational and Structural Biotechnology Journal, 2017 [link]
  4. J Dunbar, K Krawczyk, J Leem, C Marks, J Nowak, C Regep, G Georges, S Kelm, B Popovic, C M Deane - SAbPred: a structure-based antibody prediction server, Nucleic Acids Research, 2016 [link]

Background

Postdoctoral Researcher and Associate Director of the Systems Approaches to Biomedical Science CDT
University of Oxford, 2016-Present

Main research themes: analysis and structure prediction of protein loops with multiple conformations; membrane protein loop modelling; analysis of therapeutic antibodies (through supervision).

DPhil Systems Approaches to Biomedical Science
University of Oxford, 2012-2016

Thesis title: Hybrid methods for protein loop modelling

MChem (Master of Chemistry), First Class
Durham University, 2007-2011

Masters project title: Simulating photodissociation reactions of protonated aminophenols
Dissertation title: Cellular drug delivery

Other

Besides science, I enjoy:

  • Music - I play clarinet, saxophone and piano and am a member of the OUP Orchestra
  • Art and Crafts - particularly pencil drawing and crocheting
  • Reading
  • Cryptic Crosswords
  • Baking
  • Swimming

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