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Dr John Mitchell:
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Dr John Mitchell

Dr John Mitchell
Purdie Building
University of St Andrews
North Haugh
St Andrews
KY16 9ST
Fife
UK

tel: 01334 467259
fax: 01334 462595
room: 152
email: jbom@st-andrews.ac.uk

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Research group website

School of Chemistry
Biomedical Sciences Research Complex
Evolution, Genes and Genomics Group
Institute for Data-Intensive Research

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The interface between biology and chemistry is fertile ground for the development of new computational techniques. Yet it is still hard to predict protein-ligand binding, model protein folding or design effective pharmaceutical products.

Enzyme-catalysed reactions are ubiquitous and essential to the chemistry of life. Structures, gene sequences, mechanisms, metabolic pathways and kinetic data are currently spread between many different databases and throughout the literature. We have created MACiE, the world's first comprehensive electronic database of the chemical mechanisms of enzymatic reactions. We are using MACIE to investigate fundamental questions about the chemistry of enzyme functions, their evolution, and their substrate specificity. 

Improving the prediction of solubility is essential to reduce the current unacceptable attrition rate in drug development. We are developing methods to predict aqueous solubility for drug-like molecules, and hope to move on to study its dependence on pH, salt effects and crystal polymorphism. We have developed a number of predictive methods for solubility, of which the most successful is based on a Random Forest of decision trees. We are also using computational chemistry to calculate the various energy terms associated with solvation. This work spans quantum chemistry, molecular simulation, QSAR and chemical informatics.

Additional information about the current Mitchell Group can be found here: http://chemistry.st-andrews.ac.uk/staff/jbom/group/

 



The interface between biology and chemistry is fertile ground for the development of new computational techniques. Yet it is still hard to predict protein-ligand binding, model protein folding or design effective pharmaceutical products.

Enzyme-catalysed reactions are ubiquitous and essential to the chemistry of life. Structures, gene sequences, mechanisms, metabolic pathways and kinetic data are currently spread between many different databases and throughout the literature. We have created MACiE, the world's first comprehensive electronic database of the chemical mechanisms of enzymatic reactions. We are using MACIE to investigate fundamental questions about the chemistry of enzyme functions, their evolution, and their substrate specificity.

Improving the prediction of solubility is essential to reduce the current unacceptable attrition rate in drug development. We are developing methods to predict aqueous solubility for drug-like molecules, and hope to move on to study its dependence on pH, salt effects and crystal polymorphism. We have developed a number of predictive methods for solubility, of which the most successful is based on a Random Forest of decision trees. We are also using computational chemistry to calculate the various energy terms associated with solvation. This work spans quantum chemistry, molecular simulation, QSAR and chemical informatics.

Additional information about the current Mitchell Group can be found here: http://chemistry.st-andrews.ac.uk/staff/jbom/group/

Ph.D. studentships in Modelling the Evolution of Enzyme Catalysis and Computing Aqueous Solubility and Understanding Hydrophobicity are now available.

Selected Recent Publications

DS Palmer, A Llinàs, I Morao, GM Day, JM Goodman, RC Glen & JBO Mitchell, Molecular Pharmaceutics, (2008), 5, 266-279

NM O'Boyle, GL Holliday, DE Almonacid & JBO Mitchell, Journal of Molecular Biology, (2007), 368, 1484-1499

GL Holliday, DE Almonacid, GJ Bartlett, NM O'Boyle, JW Torrance, P Murray-Rust, JBO Mitchell & JM Thornton, Nucleic Acids Research, (2007), 35, D515-D520

GL Holliday, DE Almonacid, JBO Mitchell & JM Thornton, Journal of Molecular Biology, (2007), 372, 1261-1277

DS Palmer, NM O'Boyle, R C Glen & JBO Mitchell, Journal of Chemical Information and Modeling, (2007), 47, 150-158

source: symbiosis


Recent Publications:

5 (of 116 /dk/atira/pure/researchoutput/status/published available) for jbom (source: University of St Andrews PURE)
Please click title of any item for full details

Cooperative coinfection dynamics on clustered networks P. Mann, V Anne Smith, John B. O. Mitchell, Simon Andrew Dobson
Physical Review. E, Statistical, nonlinear, and soft matter physics 2021 vol. 103
Exact formula for bond percolation on cliques V Anne Smith, John B. O. Mitchell, Christopher Anthony Jefferson, Simon Andrew Dobson
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 2021 vol. 104
Percolation in random graphs with higher-order clustering V Anne Smith, John B. O. Mitchell, Simon Andrew Dobson
Physical Review. E, Statistical, nonlinear, and soft matter physics 2021 vol. 103
Random graphs with arbitrary clustering and their applications V Anne Smith, John B. O. Mitchell, Simon Andrew Dobson
Physical Review. E, Statistical, nonlinear, and soft matter physics 2021 vol. 103
Symbiotic and antagonistic disease dynamics on clustered networks using bond percolation V Anne Smith, John B. O. Mitchell, Simon Andrew Dobson
Physical Review. E, Statistical, nonlinear, and soft matter physics 2021 vol. 104