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The University of Southampton

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Phone:: (023) 8059 2794
Email:: J.W.Essex@soton.ac.uk

Professor Jonathan W Essex BA (MA) DPhil

Professor of Computational Systems Chemistry, Director of Research

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 Chemistry Central. In addition, he serves on the Management 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

2003-2008 “Basic Technology: 4 Billion Bases a Day – Practical Individual Genome Sequencing”, EPSRC, £5033k. Collaborative grant with M. Bradley, J.A.C. Bland, N.I. Zheludev, A. Prugel-Bennett, P. Roach, I.S. Nandhakumar, A.H. Welsh, D.C. Neylon

2004-2008 “IntBioSim: An Integrated Approach to Multi-Level Biomolecular Simulations”, BBSRC, £976k. Collaborative grant with M.S.P. Sansom, A.J. Mulholland, P. Coveney, D. Gavaghan, J. Gurd, S. McKeever

2005-2010 “PLATFORM: End-to-End Pipeline for Chemical Information: From the Laboratory to Literature and Back Again”, EPSRC, £415k. Collaborative grant with J.G. Frey, D. Woods, D. De Roure, M. Hursthouse, S. Lewis, J. Owen, S. Sahu, L. Moreau, M. Surridge, M. Schraefel

2005-2008 “A CCP to Build Capacity and Capability in Biomolecular Simulation”, BBSRC, £147k. Collaborative grant with C.A. Laughton, A.J. Mulholland, M.S.P. Sansom

2006-2009 “Coarse-Grained Simulations for Membranes and Membrane Proteins: Rafts, Folding and Fusion”, BBSRC, £385k. Collaborative grant with M.S.P. Sansom

Research group

Computational Systems Chemistry

Research project(s)

Essex: The simulation of protein-ligand systems

Essex: The simulation of rare conformational change events in proteins

Essex: Cheminformatics, Bioinformatics and Education

Essex: The simulation of biological membranes

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Key Publications

Orsi, M., Sanderson, W. E., & Essex, J. W. (2009). Permeability of small molecules through a lipid bilayer: a multiscale simulation study. The Journal of Physical Chemistry B, 113(35), 12019-12029. DOI: 10.1021/jp903248s
Weber, G., Essex, J. W., & Neylon, C. (2009). Probing the microscopic flexibility of DNA from melting temperatures. Nature Physics, 5(10), 769-773. DOI: 10.1038/NPHYS1371
Michel, J., & Essex, J. W. (2008). Hit identification and binding mode predictions by rigorous free energy simulations. Journal of Medicinal Chemistry, 51(21), 6654-6664. DOI: 10.1021/jm800524s
Orsi, M., Haubertin, D. Y., Sanderson, W. E., & Essex, J. W. (2008). A quantitative coarse-grain model for lipid bilayers. The Journal of Physical Chemistry B, 112(3), 802-815. DOI: 10.1021/jp076139e

Articles

Sutton, E. J., Bradshaw, R., Orr, C., Frendéus, B., Larsson, G., Teige, I., ... Essex, J. W. (2018). Evaluating anti-CD32b F(ab) conformation using molecular dynamics and small-angle X-ray scattering. Biophysical Journal, 115(2), 289-299. DOI: 10.1016/j.bpj.2018.03.040
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. DOI: 10.1038/s42004-018-0019-x
Saunders, G. M., Bruce Macdonald, H. E., Essex, J. W., & Khalid, S. (2018). Prediction of the closed conformation and insights into the mechanism of the membrane enzyme LpxR. Biophysical Journal, 1-12. DOI: 10.1016/j.bpj.2018.09.002
Longford, F. G. J., Essex, J. W., Skylaris, C-K., & Frey, J. G. (2018). Unexpected finite size effects in interfacial systems: why bigger is not always better - increase in uncertainty of surface tension with bulk phase width. The Journal of Chemical Physics, 148(21), 1-12. [214704]. DOI: 10.1063/1.5025887
Chancellor, A., Tocheva, A., Cave-Ayland, C., Tezera, L. B., White, A., Al Dulayymi, J., ... 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. DOI: 10.1073/pnas.1708252114
Haensele, E., Mele, N., Miljak, M., Read, C. M., Whitley, D. C., Banting, L., ... Clark, T. (2017). Conformation and dynamics of human urotensin II and urotensin related peptide in aqueous solution. Journal of Chemical Information and Modeling, 1-13. DOI: 10.1021/acs.jcim.6b00706
Genheden, S., Essex, J., & Lee, A. (2017). G protein coupled receptor interactions with cholesterol deep in the membrane. Biochimica et Biophysica Acta (BBA) - Biomembranes, 1859(2), 268-281. DOI: 10.1016/j.bbamem.2016.12.001
Piggot, T. J., Allison, J. R., Sessions, R. B., & Essex, J. W. (2017). On the calculation of acyl chain order parameters from lipid simulations. Journal of Chemical Theory and Computation. DOI: 10.1021/acs.jctc.7b00643
Graham, J. A., Essex, J., & Khalid, S. (2017). PyCGTOOL: automated generation of coarse-grained molecular dynamics models from atomistic trajectories. Journal of Chemical Information and Modeling, 57(4), 650-656. DOI: 10.1021/acs.jcim.7b00096
Ross, G. A., Bruce Macdonald, H. E., Cave-Ayland, C., Cabedo Martinez, A. I., & Essex, J. W. (2017). Replica-Exchange and Standard State Binding Free Energies with Grand Canonical Monte Carlo. Journal of Chemical Theory and Computation, 12(13), 6373–6381. DOI: 10.1021/acs.jctc.7b00738
Cave-Ayland, C., Skylaris, C., & Essex, J. (2016). A Monte Carlo Resampling approach for the calculation of hybrid classical and quantum free energies. Journal of Chemical Theory and Computation, 1-10. DOI: 10.1021/acs.jctc.6b00506
Albaugh, A., Boateng, H. A., Bradshaw, R., Demerdash, O. N., Dziedzic, J., Mao, Y., ... Head-Gordon, T. (2016). Advanced potential energy surfaces for molecular simulation. The Journal of Physical Chemistry B, 120(37), 9811-9832. DOI: 10.1021/acs.jpcb.6b06414
Genheden, S., & Essex, J. (2016). All-atom/coarse-grained hybrid predictions of distribution coefficients in SAMPL5. Journal of Computer-Aided Molecular Design, 1-8. DOI: 10.1007/s10822-016-9926-z
Mansour, S., Tocheva, A., Cave-Ayland, C., Machelett, M. M., Sander, B., Lissin, N. M., ... Gadola, S. D. (2016). Cholesteryl esters stabilise human CD1c conformations for recognition by self-reactive T cells. Proceedings of the National Academy of Sciences, 113(9), E1266-E1275. DOI: 10.1073/pnas.1519246113, 10.1073/pnas.1519246113
Bradshaw, R. T., & Essex, J. W. (2016). Evaluating parameterization protocols for hydration free energy calculations with the AMOEBA polarizable force field. Journal of Chemical Theory and Computation, 12(8), 3871-3883. DOI: 10.1021/acs.jctc.6b00276
Mohamed, N., Bradshaw, R., & Essex, J. (2016). Evaluation of solvation free energies for small molecules with the AMOEBA polarizable force field. Journal of Computational Chemistry, 37(32), 2749-2758. DOI: 10.1002/jcc.24500
Ouaray, Z., ElSawy, K. M., Lane, D. P., Essex, J., & Verma, C. (2016). Reactivation of mutant p53: Constraints on mechanism highlighted by principal component analysis of the DNA binding domain. Proteins: Structure, Function, and Bioinformatics, 84(10), 1443-1461. DOI: 10.1002/prot.25089
Fox, S. J., Gourdain, S., Coulthurst, A., Fox, C., Kuprov, I., Essex, J. W., ... Linclau, B. (2015). A computational study of vicinal fluorination in 2,3-difluorobutane: implications for conformational control in alkane chains. Chemistry - A European Journal, 21, 1682-1691. DOI: 10.1002/chem.201405317
Genheden, S., & Essex, J. W. (2015). A simple and transferable all-atom/coarse-grained hybrid model to study membrane processes. Journal of Chemical Theory and Computation, 11(10), 4749-4759. DOI: 10.1021/acs.jctc.5b00469
Cave-Ayland, C., Skylaris, C-K., & Essex, J. W. (2015). Direct validation of the single step classical to quantum free energy perturbation. The Journal of Physical Chemistry B, 119(3), 1017-1025. DOI: 10.1021/jp506459v
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. DOI: 10.1021/jacs.5b07940
Dinis, P., Suess, D. L. M., Fox, S. J., Harmer, J. E., Driesener, R. C., De La Paz, L., ... 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. DOI: 10.1073/pnas.1417252112
Genheden, S., Cabedo Martinez, A. I., Criddle, M. P., & Essex, J. W. (2014). Extensive all-atom Monte Carlo sampling and QM/MM corrections in the SAMPL4 hydration free energy challenge. Journal of Computer-Aided Molecular Design, 28(3), 187-200. DOI: 10.1007/s10822-014-9717-3
Bodnarchuk, M. S., Viner, R., Michel, J., & Essex, J. W. (2014). Strategies to calculate water binding free energies in protein–ligand complexes. Journal of Chemical Information and Modeling, 54(6), 1623-1633. DOI: 10.1021/ci400674k
Harmer, J., Hiscox, M. J., Dinis, P. C., Fox, S. J., Iliopoulos, A., Hussey, J. E., ... Roach, P. L. (2014). Structures of lipoyl synthase reveal a compact active site for controlling sequential sulfur insertion reactions. Biochemical Journal, 464(1), 123-133. DOI: 10.1042/BJ20140895
Fox, S. J., Pittock, C., Tautermann, C. S., Fox, T., Christ, C., Malcolm, N. O. J., ... Skylaris, C-K. (2013). Free energies of binding from large-scale first-principles quantum mechanical calculations: application to ligand hydration energies. The Journal of Physical Chemistry B, 117(32), 9478-9485. DOI: 10.1021/jp404518r
Bortolato, A., Tehan, B. G., Bodnarchuk, M. S., Essex, J. W., & Mason, J. S. (2013). Water network perturbation in ligand binding: Adenosine A2AAntagonists as a case study. Journal of Chemical Information and Modeling, 53(7), 1700-1713. DOI: 10.1021/ci4001458
Orsi, M., & Essex, J. W. (2012). Physical properties of mixed bilayers containing lamellar and nonlamellar lipids: insights from coarse-grain molecular dynamics simulations. Faraday Discussions, 161, 249-272. DOI: 10.1039/C2FD20110K
Beierlein, F. R., Michel, J., & Essex, J. W. (2011). A simple QM/MM approach for capturing polarization effects in protein?ligand binding free energy calculations. The Journal of Physical Chemistry B, 115(17), 4911-4926. DOI: 10.1021/jp109054j
Craig, I. R., Pfleger, C., Gohlke, H., Essex, J. W., & Spiegel, K. (2011). Pocket-space maps to identify novel binding-site conformations in proteins. Journal of Chemical Information and Modeling, 51(10), 2666-2679. DOI: 10.1021/ci200168b
Warenius, H. M., Kilburn, J. D., Essex, J. W., Maurer, R. I., Blaydes, J. P., Agarwala, U., & Seabra, L. A. (2011). Selective anticancer activity of a hexapeptide with sequence homology to a non-kinase domain of Cyclin Dependent Kinase 4. Molecular Cancer, 10(1), 72-[54pp]. DOI: 10.1186/1476-4598-10-72
Fraternali, F. (Ed.), Orsi, M., & Essex, J. W. (2011). The ELBA force field for coarse-grain modeling of lipid membranes. PLoS ONE, 6(12), e28637. DOI: 10.1371/journal.pone.0028637
Deriu, M. A., Soncini, M., Orsi, M., Patel, M., Essex, J. W., Montevecchi, F. M., & Redaelli, A. (2010). Anisotropic elastic network modeling of entire microtubules. Biophysical Journal, 99(7), 2190-2199. DOI: 10.1016/j.bpj.2010.06.070
Orsi, M., Michel, J., & Essex, J. W. (2010). Coarse-grain modelling of DMPC and DOPC lipid bilayers. Journal of Physics: Condensed Matter, 22(15), 155106. DOI: 10.1088/0953-8984/22/15/155106
Orsi, M., Noro, M. G., & Essex, J. W. (2010). Dual-resolution molecular dynamics simulation of antimicrobials in biomembranes. Journal of the Royal Society Interface. DOI: 10.1098/rsif.2010.0541
Craig, I. R., Essex, J. W., & Spiegel, K. (2010). Ensemble docking into multiple crystallographically derived protein structures: an evaluation based on the statistical analysis of enrichments. Journal of Chemical Information and Modeling, 50(4), 511-524. DOI: 10.1021/ci900407c
Orsi, M., & Essex, J. W. (2010). Permeability of drugs and hormones through a lipid bilayer: insights from dual-resolution molecular dynamics. Soft Matter, 6(16), 3797-3808. DOI: 10.1039/c0sm00136h
Michel, J., & Essex, J. W. (2010). Prediction of protein–ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations. Journal of Computer-Aided Molecular Design, 24(8), 639-658. DOI: 10.1007/s10822-010-9363-3
Michel, J., Foloppe, N., & Essex, J. W. (2010). Rigorous free energy calculations in structure-based drug design. Molecular Informatics, 29(8-9), 570-578. DOI: 10.1002/minf.201000051
Cossins, B. P., Foucher, S., Edge, C. M., & Essex, J. W. (2009). Assessment of nonequilibrium free energy methods. The Journal of Physical Chemistry B, 113(16), 5508-5519. DOI: 10.1021/jp803532z
Wiley, A. P., Williams, S. L., & Essex, J. W. (2009). Conformational motions of HIV-1 protease identified using reversible digitally filtered molecular dynamics. Journal of Chemical Theory and Computation, 5(4), 1117-1128. DOI: 10.1021/ct800152d
Orsi, M., Sanderson, W. E., & Essex, J. W. (2009). Permeability of small molecules through a lipid bilayer: a multiscale simulation study. The Journal of Physical Chemistry B, 113(35), 12019-12029. DOI: 10.1021/jp903248s
Weber, G., Essex, J. W., & Neylon, C. (2009). Probing the microscopic flexibility of DNA from melting temperatures. Nature Physics, 5(10), 769-773. DOI: 10.1038/NPHYS1371
Williams, S. L., & Essex, J. W. (2009). Study of the conformational dynamics of the catalytic loop of WT and G140A/G149A HIV-1 integrase core domain using reversible digitally filtered molecular dynamics. Journal of Chemical Theory and Computation, 5(2), 411-421. DOI: 10.1021/ct800162v
Weber, G., Haslam, N., Essex, J. W., & Neylon, C. (2009). Thermal equivalence of DNA duplexes for probe design. Journal of Physics: Condensed Matter, 21(3), 34106. DOI: 10.1088/0953-8984/21/3/034106
Orsi, M., Haubertin, D. Y., Sanderson, W. E., & Essex, J. W. (2008). A quantitative coarse-grain model for lipid bilayers. The Journal of Physical Chemistry B, 112(3), 802-815. DOI: 10.1021/jp076139e
Michel, J., & Essex, J. W. (2008). Hit identification and binding mode predictions by rigorous free energy simulations. Journal of Medicinal Chemistry, 51(21), 6654-6664. DOI: 10.1021/jm800524s
Haslam, N. J., Whiteford, N. E., Weber, G., Prügel-Bennett, A., Essex, J. W., & Neylon, C. (2008). Optimal probe length varies for targets with high sequence variation: implications for probe library design for resequencing highly variable genes. PLoS ONE, 3(6), e2500. DOI: 10.1371/journal.pone.0002500
Hudson, B. D., Whitley, D. C., Ford, M. G., Swain, M., & Essex, J. W. (2008). Pattern recognition based on color-coded quantum mechanical surfaces for molecular alignment. Journal of Molecular Modeling, 14(1), 49-57. DOI: 10.1007/s00894-007-0251-2
Michel, J., Orsi, M., & Essex, J. W. (2008). Prediction of partition coefficients by multiscale hybrid atomic-level/coarse-grain simulations. The Journal of Physical Chemistry B, 112(3), 657-660. DOI: 10.1021/jp076142y
Cossins, B. P., Foucher, S., Edge, C. M., & Essex, J. W. (2008). Protein?ligand binding affinity by nonequilibrium free energy methods. The Journal of Physical Chemistry B, 112(47), 14985-14992. DOI: 10.1021/jp803533w
Whiteford, N. E., Haslam, N. J., Weber, G., Prügel-Bennett, A., Essex, J. W., & Neylon, C. (2008). Visualising the repeat structure of genomic sequences. Complex Systems, 17(4), 381-398.
Barillari, C., Taylor, J., Viner, R., & Essex, J. W. (2007). Classification of water molecules in protein binding sites. Journal of the American Chemical Society, 129(9), 2577-2587. DOI: 10.1021/ja066980q
Geldhill, R., Kent, S., Milsted, A., Chapman, R., Essex, J. W., & Frey, J. G. (2007). e-Malaria: the schools malaria project. Concurrency and Computation: Practice and Experience, 20(3), 225-238. DOI: 10.1002/cpe.1193
Michel, J., Verdonk, M. L., & Essex, J. W. (2007). Protein-ligand complexes: computation of the relative free energy of different scaffolds and binding modes. Journal of Chemical Theory and Computation, 3(5), 1645-1655. DOI: 10.1021/ct700081t
Tai, K., Baaden, M., Murdock, S., Wu, B., Ng, M. H., Johnston, S., ... Sansom, M. S. P. (2007). Three hydrolases and a transferase: comparative analysis of active-site dynamics via the BioSimGrid database. Journal of Molecular Graphics and Modelling, 25(6), 896-902. DOI: 10.1016/j.jmgm.2006.08.010
Gledhill, R., Kent, S., Hudson, B., Richards, W. G., Essex, J. W., & Frey, J. G. (2006). A computer-aided drug discovery system for chemistry teaching. Journal of Chemical Information and Modeling, 46(3), 960-970. DOI: 10.1021/ci050383q
Ng, M. H., Johnston, S., Wu, B., Murdock, S. E., Tai, K., Fangohr, H., ... Jeffreys, P. (2006). BioSimGrid: grid-enabled biomolecular simulation data storage and analysis. Future Generation Computer Systems, 6(22), 657-664. DOI: 10.1016/j.future.2005.10.005
Taylor, K. R., Gledhill, R., Essex, J. W., Frey, J. G., Harris, S. W., & De Roure, D. C. (2006). Bringing chemical data onto the semantic web. Journal of Chemical Information and Modeling, 46(3), 939-952. DOI: 10.1021/ci050378m
Michel, J., Taylor, R. D., Verdonk, M. L., & Essex, J. W. (2006). Calculating free energies with fast implicit solvent models. Abstracts of Papers of the American Chemical Society, 231.
Michel, J., Taylor, R. D., & Essex, J. W. (2006). Efficient generalized Born models for Monte Carlo simulations. Journal of Chemical Theory and Computation, 2(3), 732-739. DOI: 10.1021/ct600069r
Michel, J., Verdonk, M. L., & Essex, J. W. (2006). Protein-ligand binding affinity predictions by implicit solvent simulations: a tool for lead optimization? Journal of Medicinal Chemistry, 49(25), 7427-7439. DOI: 10.1021/jm061021s
Murdock, S. E., Tai, K., Ng, M. H., Johnston, S., Wu, B., Fangohr, H., ... Sansom, M. S. P. (2006). Quality assurance for biomolecular simulations. Journal of Chemical Theory and Computation, 2(6), 1477-1481. DOI: 10.1021/ct6001708
Taylor, K., Essex, J. W., Frey, J. G., Mills, H. R., Hughes, G., & Zaluska, E. J. (2006). The semantic grid and chemistry: experiences with CombeChem. Web Semantics, 4(2), 84-101. DOI: 10.1016/j.websem.2006.03.003
Weber, G., Haslam, N., Whiteford, N., Prugel-Bennett, A., Essex, J. W., & Neylon, C. (2006). Thermal equivalence of DNA duplexes without calculation of melting temperature. Nature Physics, 2(1), 55-59. DOI: 10.1038/nphys189
Whiteford, N., Haslam, N., Weber, G., Prugel-Bennett, A., Essex, J. W., Roach, P. L., ... Neylon, C. (2005). An analysis of the feasibility of short read sequencing. Nucleic Acids Research, 33(19), e171-[6pp]. DOI: 10.1093/nar/gni170
Bemporad, D., Luttmann, C., & Essex, J. W. (2005). Behaviour of small solutes and large drugs in a lipid bilayer from computer simulations. Biochimica et Biophysica Acta (BBA) - Biomembranes, 1718(1-2), 1-21. DOI: 10.1016/j.bbamem.2005.07.009
Woods, C. J., Ng, M. H., Johnston, S., Murdock, S. E., Wu, B., Tai, K., ... Essex, J. W. (2005). Grid computing and biomolecular simulation. Philosophical Transactions of The Royal Society A: Mathematical, Physical and Engineering Sciences, 363(1833), 2017-2035. DOI: 10.1098/rsta.2005.1626
Rousay, E. R., Fu, H., Robinson, J. M., Essex, J. W., & Frey, J. G. (2005). Grid-based dynamic electronic publication: a case study using combined experiment and simulation studies of crown ethers at the air/water interface. Philosophical Transactions of The Royal Society A: Mathematical, Physical and Engineering Sciences, 363(1833), 2075-2095. DOI: 10.1098/rsta.2005.1630
Dixon, M. J., Maurer, R. I., Biggi, C., Oyarzabal, J., Essex, J. W., & Bradley, M. (2005). Mechanism and structure-activity relationships of norspermidine-based peptidic inhibitors of trypanothione reductase. Bioorganic & Medicinal Chemistry, 13(14), 4513-4526.
Wiley, A. P., Swain, M. T., Phillips, S. C., Essex, J. W., & Edge, C. M. (2005). Parametrization of reversible digitally filtered molecular dynamics simulations. Journal of Chemical Theory and Computation, 1(1), 24-35. DOI: 10.1021/ct049970t S1549-9618(04)09970-9
Mansson, R. A., Frey, J. G., Essex, J. W., & Welsh, A. H. (2005). Prediction of properties from simulations: a re-examination with modern statistical methods. Journal of Chemical Information and Modeling, 45(6), 1791-1803. DOI: 10.1021/ci050056i
Wu, B., Dovey, M., Ng, M. H., Tai, K., Murdock, S., Fangohr, H., ... Sansom, M. S. P. (2004). A web/grid portal implementation of BioSimGrid: a biomolecular simulation database. Journal of Digital Information Management, 2(2), 74-78.
Essex, J. W., Woods, C. J., Willey, A. P., Fenu, L. A., Good, A. C., Leach, A. R., ... Frey, J. G. (2004). Application of distributed computing to computer simulations. Abstracts of Papers of the American Chemical Society, 227, p.U683.
Essex, J. W., Tai, K., Murdock, S., Ng, M. H., Wu, B., Johnston, S., ... Sansom, M. (2004). BioSimGrid: a distributed database for biomolecular simulations. Abstracts of Papers of the American Chemical Society, 227, U682.
Tai, K., Murdock, S., Wu, B., Ng, M. H., Johnston, S., Fangohr, H., ... Sansom, M. S. P. (2004). BioSimGrid: towards a worldwide repository for biomolecular simulations. Organic & Biomolecular Chemistry, 2(22), 3219-3221. DOI: 10.1039/b411352g
Bemporad, D., Luttmann, C., & Essex, J. W. (2004). Computer simulation of small molecule permeation across a lipid bilayer: dependence on bilayer properties and solute volume, size, and cross-sectional area. Biophysical Journal, 87(1), 1-13.
Henchman, R. H., Kilburn, J. A., Turner, D. L., & Essex, J. W. (2004). Conformational and enantioselectivity in host-guest chemistry: the selective binding of cis amides examined by free energy calculations. The Journal of Physical Chemistry B, 108(45), 17571-17582. DOI: 10.1021/jp046520o
Bemporad, D., Essex, J. W., & Luttmann, C. (2004). Permeation of small molecules through a lipid bilayer: a computer simulation study. The Journal of Physical Chemistry B, 108(15), 4875-4884. DOI: 10.1021/jp035260s
Essex, J. W., Woods, C. J., Foucher, S., & King, M. A. (2004). Replica-exchange-based free-energy methods. Abstracts of Papers of the American Chemical Society, 227, U1030-U1030.
Michel, J., Taylor, R. D., & Essex, J. W. (2004). The parameterization and validation of generalized born models using the pairwise descreening approximation. Journal of Computational Chemistry, 25(14), 1760-1770. DOI: 10.1002/jcc.20105
Phillips, S. C., Gledhill, R. J., Essex, J. W., & Edge, C. M. (2003). Application of the Hilbert-Huang transform to the analysis of molecular dynamics simulations. Journal of Physical Chemistry A, 107(24), 4869-4876. DOI: 10.1021/jp0261758
Woods, C. J., Essex, J. W., & King, M. A. (2003). Enhanced configurational sampling in binding free-energy calculations. The Journal of Physical Chemistry B, 107(49), 13711-13718. DOI: 10.1021/jp036162+
Taylor, R. D., Jewsbury, P. J., & Essex, J. W. (2003). FDS: flexible ligand and receptor docking with a continuum solvent model and soft-core energy function. Journal of Computational Chemistry, 24(13), 1637-1656. DOI: 10.1002/jcc.10295
Phillips, S. C., Swain, M. T., Wiley, A. P., Essex, J. W., & Edge, C. M. (2003). Reversible digitally filtered molecular dynamics. The Journal of Physical Chemistry B, 107(9), 2098-2110. DOI: 10.1021/jp026456f
De Luca, S., Ulhaq, S., Dixon, M. J., Essex, J., & Bradley, M. (2003). Solid-phase synthesis of a focused library of trypanothione reductase inhibitors. Tetrahedron Letters, 44(15), 3195-3197. DOI: 10.1016/S0040-4039(03)00438-6
Woods, C. J., Essex, J. W., & King, M. A. (2003). The development of replica-exchange-based free-energy methods. The Journal of Physical Chemistry B, 107(49), 13703-13710. DOI: 10.1021/jp0356620
Taylor, R. D., Jewsbury, P. J., & Essex, J. W. (2002). A review of protein-small molecule docking methods. Journal of Computer-Aided Molecular Design, 16(3), 151-166. DOI: 10.1023/A:1020155510718
Essex, J. W., Phillips, S. C., Gledhill, R. J., & Edge, C. M. (2002). Digital signal processing methods to analyze and enhance conformational change. Abstracts of Papers of the American Chemical Society, 223, U467-U467.
Woods, C. J., Camiolo, S., Light, M. E., Coles, S. J., Hursthouse, M. B., King, M. A., ... Essex, J. W. (2002). Fluoride-selective binding in a new deep cavity calix[4]pyrrole: experiment and theory. Journal of the American Chemical Society, 124(29), 8644-8652. DOI: 10.1021/ja025572t
Whitehead, L., Edge, C. M., & Essex, J. W. (2001). Molecular dynamics simulation of the hydrocarbon region of a biomembrane using a reduced representation model. Journal of Computational Chemistry, 22(14), 1622-1633. DOI: 10.1002/jcc.1118
Woods, C. J., King, M. A., & Essex, J. W. (2001). The configurational dependence of binding free energies: a Poisson-Boltzmann study of Neuraminidase inhibitors. Journal of Computer-Aided Molecular Design, 15(2), 129-144. DOI: 10.1023/A:1008197913568
Phillips, S. C., Essex, J. W., & Edge, C. M. (2000). Digitally filtered molecular dynamics: the frequency specific control of molecular dynamics simulations. The Journal of Chemical Physics, 112(6), 2586-2597. DOI: 10.1063/1.480832
Bartlett, P. N., Essex, J. W., Koo, H. J. I. S., Robertson, N., & Whangbo, M. H. (2000). Molecular self-assembly on surfaces of organic conducting salts: Epitaxial monolayer films of naphthalene on the (001) surface of (TMTSF)(2)PF6. The Journal of Physical Chemistry B, 104(31), 7394-7402. DOI: 10.1021/jp000013z

Book Chapter

Frey, J. G., Bradley, M., Essex, J., Hursthouse, M. B., Lewis, S. M., Luck, M. 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). Chichester, UK: John Wiley & Sons, Ltd..

Conferences

Frey, J. G., Gledhill, R. J., Milsted, A., Kent, S., Essex, J. W., & Richards, G. W. (2006). A computer-aided drug discovery system for chemistry teaching. American Chemical Society 232 National Meeting, .
Frey, J., De Roure, D., Taylor, K., Essex, J., Mills, H., & Zaluska, E. (2006). CombeChem: a case study in provenance and annotation using the Semantic Web. In L. Moreau, & I. Foster (Eds.), Provenance and Annotation of Data (pp. 270-277). (Lecture Notes in Computer Science; Vol. 4145/2006). Berlin, Germany: Springer. DOI: 10.1007/11890850_27
Frey, J. G., Gledhill, R., Kent, S., Hudson, B., & Essex, J. (2006). Schools Malaria Project. In Proceedings of the UK e-Science All Hands Meeting 2005 (UK e-Science All Hands Meeting; No. 2005). UK: Engineering and Physical Science Research Council.
Wu, B., Tai, K., Ng, M. H., Johnston, S., Murdock, S., Fangohr, H., ... Cox, S. (2005). Towards a grid-enabled biomolecular simulation database. In Proceedings of the UK e-Science All Hands Meeting 2005 (pp. 4pp). Swindon, UK: Engineering and Physical Sciences Research Council.
Wu, B., Dovey, M., Ng, M. H., Tai, K., Murdock, S., Jeffreys, P., ... Sansom, M. S. P. (2004). A web/grid portal implementation of BioSimGrid: a biomolecular simulation database. In P. K. Srimani (Ed.), Proceedings ITCC 2004: International Conference on Information Technology: Coding and Computing (pp. 50-54). Los Alamitos, USA: IEEE Computer Society. DOI: 10.1109/ITCC.2004.1286589
Woods, C., Gledhill, R., Williams, S., & Essex, J. (2004). Distributed Computing. EPSRC eScience Pilot Project Meeting, .
Ng, M. H., Johnston, S., Murdock, S., Wu, B., Tai, K., Fangohr, H., ... Jeffreys, P. (2004). Efficient data storage and analysis for generic biomolecular simulation data. 443-450. Paper presented at 3rd UK e-Science Programme All Hands Meeting (AHM 2004), .
Robinson, J., Grove, D., Lewis, S., Manson, R., Frey, J., Essex, J., ... Parry, P. (2004). eTechniques for Teaching. EPSRC eScience Testbed projects meeting, .
Welsh, A., Mansson, R., Danos, L., Frey, J., & Essex, J. (2004). Statistical Model Fitting. EPSRC eScience Pilot Project Meeting, .
Woods, C. J., Frey, J. G., & Essex, J. W. (2004). The Application of Distributed Computing to the Investigation of Protein Conformational Change. In S. Cox (Ed.), Proceedings of the UK e-Science All Hands Meeting, Sep 2003 (pp. (6pp)). Swindon, UK: EPSRC.
Wu, B., Tai, K., Murdock, S., Ng, M. H., Johnston, S., Fangohr, H., ... Sansom, M. S. P. (2003). BioSimGrid: a distributed database for biomolecular simulations. In S. J. Cox (Ed.), Proceedings of UK e-Science All Hands Meeting 2003 (pp. 8pp). Swindon, UK: Engineering and Physical Sciences Research Council.

Report

Wu, B., Dovey, M., Tai, K., Ng, M. H., Murdock, S., Fangohr, H., ... 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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