Mitchell Group
Group Highlights
We are an Informatics and Computational Chemistry research group. Our group is based in the Purdie building on the North Haugh in St Andrews. Research areas we are interested in are machine learning, aqueous solubility, enzyme catalysis, protein-ligand interactions, modelling epidemics, molecular evolution and structural bioinformatics, computational toxicology, prediction of solubility and other molecular properties, and the classification of drugs used for doping in sport.
Research
- Combining Theoretical Chemistry and Machine Learning to Understand and Predict Enzyme Function;
- Computational Approaches for Enzyme Redesign;
- Computational Modelling of the Effects of Vaccines;
- Machine Learning for Prediction of Aqueous Solubility.
Group Members
John Mitchell;
Eugene Shrimpton-Phoenix;
Ben Connaughton;
Ben Read.
Publications
Chapters
In silico methods to predict solubility
McDonagh, J., Mitchell, J. B. O., Palmer, D. & Skyner, R. E., 20 Jan 2020, Solubility in Pharmaceutical Chemistry. Saal, C. & Nair, A. (eds.). de Gruyter, p. 71-112 42 p.
Research output: Chapter in Book/Report/Conference proceeding › Chapter
Classifying the world anti-doping agency's 2005 prohibited list using the Chemistry Development Kit fingerprint
Cannon, E. O. & Mitchell, J. B. O., 2006, Computational Life Sciences II: Second International Symposium, CompLife 2006, Cambridge, UK, September 27-29, 2006, Proceedings. Berthold, M. R., Glen, R. & Fischer, I. (eds.). Springer, p. 173-182 10 p. (Lecture Notes in Computer Science; vol. 4216).
Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
Modelling the interactions of protein side-chains
Mitchell, J. B. O., THORNTON, J. M. & PRICE, S. L., 1995, Modelling of biomolecular structures and mechanisms: proceedings of the Twenty-seventh Jerusalem symposium on quantum chemistry and biochemistry held in Jerusalem, Israel, May 23-26, 1994. Pullman, A., Jortner, J. & Pullman, B. (eds.). Kluwer Academic Publishers, p. 119-135 17 p. (Jerusalem symposia on quantum chemistry and biochemistry ; vol. 27).
Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
Articles
Allosteric activation unveils protein-mass modulation of ATP phosphoribosyltransferase product release
Read, B., Mitchell, J. B. O. & da Silva, R. G., 6 Apr 2024, In: Communications Chemistry. 7, 13 p., 77.
Research output: Contribution to journal › Article › peer-review
Crystal structure, steady-state and pre-steady-state kinetics of Acinetobacter baumannii ATP phosphoribosyltransferase
Read, B., Cadzow, A., Alphey, M. S., Mitchell, J. B. O. & da Silva, R. G., 16 Jan 2024, In: Biochemistry. 63, 2, p. 230-240 11 p.
Research output: Contribution to journal › Article › peer-review
Robust identification of interactions between heat-stress responsive genes in the chicken brain using Bayesian networks and augmented expression data
Videla Rodriguez, E. A., Mitchell, J. B. O. & Smith, V. A., 2 Apr 2024, (Accepted/In press) In: Scientific Reports.
Research output: Contribution to journal › Article › peer-review
A Bayesian network structure learning approach to identify genes associated with stress in spleens of chickens
Videla Rodriguez, E. A., Mitchell, J. B. O. & Smith, V. A., 6 May 2022, In: Scientific Reports. 12, 8 p., 7482.
Research output: Contribution to journal › Article › peer-review
Allosteric inhibition of Acinetobacter baumannii ATP phosphoribosyltransferase by protein:dipeptide and protein:protein Interactions
Read, B. J., Fisher, G., Wissett, O. L. R., Machado, T. F. G., Nicholson, J., Mitchell, J. B. O. & da Silva, R. G., 14 Jan 2022, In: ACS Infectious Diseases. 8, 1, p. 197-209 13 p.
Research output: Contribution to journal › Article › peer-review
Computational insights into the catalytic mechanism of is-PETase: an enzyme capable of degrading poly(ethylene) terephthalate
Shrimpton-Phoenix, E., Mitchell, J. B. O. & Buehl, M., 15 Dec 2022, In: Chemistry - A European Journal. 28, 70, 7 p., e202201728.
Research output: Contribution to journal › Article › peer-review
Degree correlations in graphs with clique clustering
Mann, P. S., Smith, V. A., Mitchell, J. B. O. & Dobson, S. A., 30 Apr 2022, In: Physical Review. E, Statistical, nonlinear, and soft matter physics. 105, 4, 14 p., 044314.
Research output: Contribution to journal › Article › peer-review
N-strain epidemic model using bond percolation
Mann, P. S., Smith, V. A., Mitchell, J. B. O. & Dobson, S. A., 20 Jul 2022, In: Physical Review. E, Statistical, nonlinear, and soft matter physics. 106, 1, 20 p., 014304.
Research output: Contribution to journal › Article › peer-review
Practical application of a Bayesian network approach to poultry epigenetics and stress
Videla Rodriguez, E. A., Pértille, F., Guerrero-Bosagna, C., Mitchell, J. B. O., Jensen, P. & Smith, V. A., 1 Jul 2022, In: BMC Bioinformatics. 23, 16 p., 261.
Research output: Contribution to journal › Article › peer-review
Cooperative coinfection dynamics on clustered networks
Mann, P., Smith, V. A., Mitchell, J. B. O. & Dobson, S., 9 Apr 2021, In: Physical Review E. 103, 4, 042307.
Research output: Contribution to journal › Article › peer-review
Other publications
Applications of crystal structure prediction – inorganic and network structures: general discussion
Burger, V., Claeyssens, F., Davies, D. W., Day, G. M., Dyer, M. S., Hare, A., Li, Y., Mellot-draznieks, C., Mitchell, J. B. O., Mohamed, S., Oganov, A. R., Price, S. L., Ruggiero, M., Ryder, M. R., Sastre, G., Schön, J. C., Spackman, P., Woodley, S. M. & Zhu, Q., 9 Oct 2018, In: Faraday Discussions. 211, p. 613-642
Research output: Contribution to journal › Comment/debate › peer-review
Applications of crystal structure prediction – organic molecular structures: general discussion
Adjiman, C., Brandenburg, J. G., Braun, D. E., Cole, J., Collins, C., Cooper, A. I., Cruz-Cabeza, A., Day, G., Dudek, M., Hare, A., Iuzzolino, L., McKay, D., Mitchell, J. B. O., Mohamed, S., Neelamraju, S., Neumann, M., Lill, S. N., Nyman, J., Oganov, A. R., Price, S. L., & 9 others , 4 Oct 2018, In: Faraday Discussions. 211, p. 493-539
Research output: Contribution to journal › Comment/debate › peer-review
Artificial intelligence in pharmaceutical research and development
Mitchell, J. B. O., Jul 2018, In: Future Medicinal Chemistry. 10, 13, p. 1529-1531 3 p.
Research output: Contribution to journal › Editorial › peer-review
Crystal structure evaluation: calculating relative stabilities and other criteria: general discussion
Addicoat, M., Adjiman, C. S., Arhangelskis, M., Beran, G. J. O., Bowskill, D., Brandenburg, J. G., Braun, D. E., Burger, V., Cole, J., Cruz-Cabeza, A. J., Day, G. M., Deringer, V. L., Guo, R., Hare, A., Helfferich, J., Hoja, J., Iuzzolino, L., Jobbins, S., Marom, N., McKay, D., & 21 others , 10 Oct 2018, In: Faraday Discussions. 211, p. 325-381
Research output: Contribution to journal › Comment/debate › peer-review
Erratum to: Predicting Melting Points of Organic Molecules: Applications to Aqueous Solubility Prediction Using the General Solubility Equation (Molecular Informatics, 2015, 34, 11, (715-724), 10.1002/minf.201500052)
McDonagh, J. L., van Mourik, T. & Mitchell, J. B. O., 1 Oct 2016, In: Molecular Informatics. 1 p.
Research output: Contribution to journal › Comment/debate › peer-review
Erratum: "in silico target predictions: Defining a benchmarking data set and comparison of performance of the multiclass naïve bayes and parzen-rosenblatt window"
Koutsoukas, A., Lowe, R., Kalantarmotamedi, Y., Mussa, H. Y., Klaffke, W., Mitchell, J. B. O., Glen, R. C. & Bender, A., 28 Jul 2014, In: Journal of Chemical Information and Modeling. 54, 7, p. 2180-2182 3 p.
Research output: Contribution to journal › Comment/debate › peer-review
Communication and re-use of chemical information in bioscience
Murray-Rust, P., Mitchell, J. B. O. & Rzepa, H. S., 18 Jul 2005, In: BMC Bioinformatics. 6, 15 p., 180.
Research output: Contribution to journal › Editorial › peer-review
AMINO AROMATIC INTERACTIONS
Mitchell, J. B. O., NANDI, C. L., ALI, S., MCDONALD, J. K., THORNTON, J. M., PRICE, S. L. & SINGH, J., 2 Dec 1993, In: Nature. 366, 6454, p. 413-413 1 p.
Research output: Contribution to journal › Letter › peer-review
Contact
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