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

Rational drug design of antineoplastic agents using 3D-QSAR, cheminformatic, and virtual screening approaches Jelica Vucicevic, Katarina Nikolic, John B. O. Mitchell
Current Medicinal Chemistry 2019 vol. 26 pp. 3874-3889
Applications of crystal structure prediction – inorganic and network structures: general discussion Virginia Burger, Frederik Claeyssens, Daniel W. Davies, Graeme M. Day, Matthew S. Dyer, Alan Hare, Yi Li, Caroline Mellot-draznieks, John B. O. Mitchell, Sharmarke Mohamed, Artem R. Oganov, Sarah L. Price, Michael Ruggiero, Matthew R. Ryder, German Sastre, J. Christian Schön, Peter Spackman, Scott M. Woodley, Qiang Zhu
Faraday Discussions 2018 vol. 211 pp. 613-642
Applications of crystal structure prediction – organic molecular structures Claire Adjiman, Jan Gerit Brandenburg, Doris E. Braun, Jason Cole, Christopher Collins, Andrew I. Cooper, Aurora Cruz-Cabeza, Graeme Day, Marta Dudek, Alan Hare, Luca Iuzzolino, David McKay, John B. O. Mitchell, Sharmarke Mohamed, Sridhar Neelamraju, Marcus Neumann, Sten Nilsson Lill, Jonas Nyman, Artem R. Oganov, Sarah Price, Angeles Pulido, Susan Reutzel-Edens, Ivo Rietveld, Michael T. Ruggiero, J. Christian Schön, Seji Tsuzuki, Joost van den Ende, Grahame Woollam, Qiang Zhu
Faraday Discussions 2018 vol. 211 pp. 493-539
Artificial intelligence in pharmaceutical research and development John B. O. Mitchell
Future Medicinal Chemistry 2018 vol. 10 pp. 1529-1531
Crystal structure evaluation: calculating relative stabilities and other criteria Matthew Addicoat, Claire S. Adjiman, Mihails Arhangelskis, Gregory J. O. Beran, David Bowskill, Jan Gerit Brandenburg, Doris E. Braun, Virginia Burger, Jason Cole, Aurora J. Cruz-Cabeza, Graeme Day, Volker L. Deringer, Rui Guo, Alan Hare, Julian Helfferich, Johannes Hoja, Luca Iuzzolino, Samuel Jobbins, Noa Marom, David McKay, John B. O. Mitchell, Sharmarke Mohamed, Marcus Neumann, Sten Nilsson Lill, Jonas Nyman, Artem R. Oganov, Pablo Piaggi, Sarah Price, Susan Reutzel-Edens, Ivo Rietveld, Michael Ruggiero, Matthew R. Ryder, German Sastre, J. Christian Schön, Christopher Taylor, Alexandre Tkatchenko, Seiji Tsuzuki, Joost van den Ende, Scott M. Woodley, Grahame Woollam, Qiang Zhu
Faraday Discussions 2018 vol. 211 pp. 325-381