Professor Jonathan W Essex BA (MA) DPhil

Head of Chemistry, Professor of Computational Systems Chemistry

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Professor Jonathan W Essex is Professor of Computational Systems Chemistry within Chemistry at the University of Southampton.

Jonathan Essex was an undergraduate at Oriel College, Oxford, and graduated with a first class honours degree in Chemistry in 1989. He then studied for a D.Phil. in computational modelling under the supervision of Prof W.G. Richards at the same institution. During his postgraduate degree he was supported by a Glaxo Research Scholarship. Having obtained his D.Phil. in 1992, he took up an SERC/NATO Postdoctoral Fellowship in the group of Prof W.L. Jorgensen at Yale University. In 1994 he returned to the UK to the University of Southampton as a Royal Society University Research Fellow. He was appointed Lecturer in 1997, Senior Lecturer in 2001, Reader in 2005 and to a Personal Chair in 2007.

Jon was awarded the 2002 Marlow Medal from the Royal Society of Chemistry for his work in the development of techniques and application of molecular simulations to the study of proteins and related systems of biological importance. He was awarded a Royal Society Wolfson Research Merit Award in 2013. He is an Editorial Board member of the Journal of Computer Aided Molecular Design and an editorial advisor for BMC Chemistry. In addition, he serves on the Advisory Board of CCPBioSim, a collaborative chemistry project dedicated to biomolecular computer simulations, is a member of the EPSRC college, and has served on the Project Working Group for the procurement of HECToR, the UK’s next generation supercomputer.

Theory and Modelling in Chemical Sciences CDT

Research

Publications

Contact

Research interests

My research involves the application and development of computer simulation methodology to the study of organic and biological molecules, with particular emphasis on the examination of molecular association. Computer simulations are particularly important in the context of modern chemical research for a number of reasons. Their ultimate objective is clearly to make predictions, but performing a successful simulation that reproduces experimental observations also confirms and validates the underlying physical assumptions of the simulation model. Simulations also offer the ability to understand experimental observations with a resolution that, depending on the model, may be at the atomistic level. This in turn may then inspire further experiments. Computer modelling is widely used not only in the academic context, but also in industry. This is particularly the case for the pharmaceutical and agrochemical sectors, where modelling is used to assist in the discovery of new active chemical agents.

My research is predominantly directed towards the development of new theoretical approaches to simulating biological systems. Methodology development is particularly challenging, time-consuming, and risky, but despite this, I have made a number of important contributions, particularly in the area of protein-ligand free energy calculations. My research programme covers a wide-range of applications. In practice, however, the areas are interrelated and mutually supporting.

Research keywords

Molecular modelling, computer simulations, proteins, membranes, pharmaceuticals

Research funding

2013-2016 SI2-CHE: Development and Deployment of Chemical Software for Advanced Potential Energy Surfaces, EPSRC, £445398. With C. Skylaris

2014-2022 EPSRC Centre for Doctoral Training in Theory and Modelling in Chemical Sciences, EPSRC, £4455902. With D. Logan, F. Manby and M. Wilson

2017-2020 A new class of tumour-associated lipid antigens for recognition by CD1c-restricted T cells, CRUK, £301105. With S. Mansour, I. Tews, B. Linclau, T. Elliot, C.K. Skylaris

2019-2022 Predicting Skin Interactions and Permeation of Chemical Agents using Computational Modelling, EPSRC/dstl £100,000 approx.

2020-2022 Solving the sampling problem in molecular simulations by Sequential Monte Carlo, EPSRC, £201,568

Research group

Computational Systems Chemistry

Key Publications

Dinis, P., Suess, D. L. M., Fox, S. J., Harmer, J. E., Driesener, R. C., De La Paz, L., Swartz, J. R., Essex, J. W., Britt, R. D., & Roach, P. L. (2015). X-ray crystallographic and EPR spectroscopic analysis of HydG, a maturase in [FeFe]-hydrogenase H-cluster assembly. Proceedings of the National Academy of Sciences of the United States of America, 112(5), 1362-1367. https://doi.org/10.1073/pnas.1417252112
Aldeghi, M., Ross, G. A., Bodkin, M. J., Essex, J. W., Knapp, S., & Biggin, P. C. (2018). Large-scale analysis of water stability in bromodomain binding pockets with grand canonical Monte Carlo. Communications Chemistry, 1(1), [19]. https://doi.org/10.1038/s42004-018-0019-x
Chancellor, A., Tocheva, A., Cave-Ayland, C., Tezera, L. B., White, A., Al Dulayymi, J., Bridgeman, J., Tews, I., Wilson, S., Lissin, N., Tebruegge, M., Marshall, B., Sharpe, S., Elliott, T., Skylaris, C-K., Essex, J. W., Baird, M., Gadola, S. D., Elkington, P., & Mansour, S. (2017). CD1b-restricted GEM T cell responses are modulated by Mycobacterium tuberculosis mycolic acid meromycolate chains. Proceedings of the National Academy of Sciences, 114(51), E10956-E10964. https://doi.org/10.1073/pnas.1708252114
Ross, G. A., Bodnarchuk, M. S., & Essex, J. W. (2015). Water sites, networks, and free energies with grand canonical Monte Carlo. Journal of the American Chemical Society, 137(47), 14930-14943. https://doi.org/10.1021/jacs.5b07940
Mansour, S., Tocheva, A., Cave-Ayland, C., Machelett, M. M., Sander, B., Lissin, N. M., Molloy, P. E., Baird, M. S., Stubs, G., Schroder, N. W. J., Schumann, R. R., Rademann, J., Postle, A. D., Jakobsen, B. K., Marshall, B. G., Gosain, R., Elkington, P., Elliott, T., Skylaris, C-K., ... Gadola, S. D. (2016). Cholesteryl esters stabilize human CD1c conformations for recognition by self-reactive T cells. Proceedings of the National Academy of Sciences, 113(9), E1266-E1275. https://doi.org/10.1073/pnas.1519246113

Articles

Book Chapters

Glass, W. G., Essex, J. W., Fraternali, F., Marzuoli, I., Samways, M. L., Biggin, P. C., & Khalid, S. (2021). Coarse-grained molecular dynamics simulations of membrane proteins: a practical guide. In I. Schmidt-Krey , & J. C. Gumbart (Eds.), Structure and Function of Membrane Proteins (pp. 253-273). (Methods in Molecular Biology; Vol. 2302). Humana. https://doi.org/10.1007/978-1-0716-1394-8_14
Frey, J. G., Bradley, M., Essex, J., Hursthouse, M. B., Lewis, S. M., Luck, M. M., Moreau, L., De Roure, D. C., Surridge, M., & Welsh, A. (2003). Combinatorial chemistry and the Grid. In F. Berman, A. J. G. Hey, & G. C. Fox (Eds.), Grid computing: making the global infrastructure a reality (pp. 945-962). (Wiley Series in Communications Networking and Distributed Systems). John Wiley & Sons, Ltd..

Conferences

Report

Wu, B., Dovey, M., Tai, K., Ng, M. H., Murdock, S., Fangohr, H., Johnston, S., Jeffreys, P., Cox, S., Essex, J. W., & Sansom, M. S. P. (2004). Security and BioSimGrid: a biomolecular simulation database. University of York, Department of Computer Science.

Professor Jonathan W Essex
Chemistry University of Southampton Highfield Southampton SO17 1BJ

Room Number: 27/2027

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