All Stories

  1. Bands, Beets & Berries: A Quantum Study of Natural Dyes for Solar Cells.

    Article • August 2025, American Chemical Society (ACS)

    Dr John Mitchell

  2. Physics-Based Solubility Prediction for Organic Molecules

    Article • Chemical Reviews, July 2025, American Chemical Society (ACS)

    Dr John Mitchell

  3. Revisiting the Application of Machine Learning Approaches in Predicting Aqueous Solubility

    Article • ACS Omega, July 2024, American Chemical Society (ACS)

    Dr John Mitchell

  4. Robust identification of interactions between heat-stress responsive genes in the chicken brain using Bayesian networks and augmented expression data

    Article • Scientific Reports, April 2024, Springer Science + Business Media

    Dr John Mitchell

  5. Allosteric activation unveils protein-mass modulation of ATP phosphoribosyltransferase product release

    Article • Communications Chemistry, April 2024, Springer Science + Business Media

    Dr John Mitchell

  6. Crystal Structure, Steady-State, and Pre-Steady-State Kinetics of Acinetobacter baumannii ATP Phosphoribosyltransferase

    Article • Biochemistry, December 2023, American Chemical Society (ACS)

    Dr John Mitchell

  7. Computational Insights into the Catalytic Mechanism of Is‐PETase: An Enzyme Capable of Degrading Poly(ethylene) Terephthalate

    Article • Chemistry - A European Journal, October 2022, Wiley

    Dr John Mitchell

  8. N -strain epidemic model using bond percolation

    Article • Physical Review E, July 2022, American Physical Society (APS)

    Dr John Mitchell

  9. Practical application of a Bayesian network approach to poultry epigenetics and stress

    Article • BMC Bioinformatics, July 2022, Springer Science + Business Media

    Dr John Mitchell

  10. A Bayesian network structure learning approach to identify genes associated with stress in spleens of chickens

    Article • Scientific Reports, May 2022, Springer Science + Business Media

    Dr John Mitchell

  11. Degree correlations in graphs with clique clustering

    Article • Physical Review E, April 2022, American Physical Society (APS)

    Dr John Mitchell

  12. Allosteric Inhibition of Acinetobacter baumannii ATP Phosphoribosyltransferase by Protein:Dipeptide and Protein:Protein Interactions

    Article • ACS Infectious Diseases, December 2021, American Chemical Society (ACS)

    Dr John Mitchell

  13. Exact formula for bond percolation on cliques

    Article • Physical Review E, August 2021, American Physical Society (APS)

    Dr John Mitchell

  14. Symbiotic and antagonistic disease dynamics on networks using bond percolation

    Article • Physical Review E, August 2021, American Physical Society (APS)

    Dr John Mitchell

  15. Two-pathogen model with competition on clustered networks

    Article • Physical Review E, June 2021, American Physical Society (APS)

    Dr John Mitchell

  16. Toward Physics-Based Solubility Computation for Pharmaceuticals to Rival Informatics

    Article • Journal of Chemical Theory and Computation, May 2021, American Chemical Society (ACS)

    Dr John Mitchell

  17. Cooperative coinfection dynamics on clustered networks

    Article • Physical Review E, April 2021, American Physical Society (APS)

    Dr John Mitchell

  18. Percolation in random graphs with higher-order clustering

    Article • Physical Review E, January 2021, American Physical Society (APS)

    Dr John Mitchell

  19. Random graphs with arbitrary clustering and their applications

    Article • Physical Review E, January 2021, American Physical Society (APS)

    Dr John Mitchell

  20. Three machine learning models for the 2019 Solubility Challenge

    Article • ADMET & DMPK, June 2020, International Association of Physical Chemists (IAPC)

    Dr John Mitchell

  21. 3. In Silico methods to predict solubility

    Article • December 2019, De Gruyter

    Dr John Mitchell

  22. Rational Drug Design of Antineoplastic Agents Using 3D-QSAR, Cheminformatic, and Virtual Screening Approaches

    Article • Current Medicinal Chemistry, September 2019, Bentham Science Publishers

    Dr John Mitchell

  23. Artificial intelligence in pharmaceutical research and development

    Article • Future Medicinal Chemistry, July 2018, Future Science

    Dr John Mitchell

  24. Applications of crystal structure prediction – inorganic and network structures: general discussion

    Article • Faraday Discussions, January 2018, Royal Society of Chemistry

    Dr John Mitchell, Dr. Matthew R. Ryder, Dr German Sastre

  25. Applications of crystal structure prediction – organic molecular structures: general discussion

    Article • Faraday Discussions, January 2018, Royal Society of Chemistry

    Dr John Mitchell, Marta Dudek

  26. Crystal structure evaluation: calculating relative stabilities and other criteria: general discussion

    Article • Faraday Discussions, January 2018, Royal Society of Chemistry

    Dr John Mitchell, Dr. Matthew R. Ryder, Dr German Sastre

  27. Can human experts predict solubility better than computers?

    Article • Journal of Cheminformatics, December 2017, Springer Science + Business Media

    Dr John Mitchell

  28. Enzyme function and its evolution

    Article • Current Opinion in Structural Biology, December 2017, Elsevier

    Dr John Mitchell

  29. Probing the average distribution of water in organic hydrate crystal structures with radial distribution functions (RDFs)

    Article • CrystEngComm, January 2017, Royal Society of Chemistry

    Dr John Mitchell

  30. Are the Sublimation Thermodynamics of Organic Molecules Predictable?

    Article • Journal of Chemical Information and Modeling, November 2016, American Chemical Society (ACS)

    Dr John Mitchell

  31. Erratum: Predicting Melting Points of Organic Molecules: Applications to Aqueous Solubility Prediction Using the General Solubility Equation

    Article • Molecular Informatics, October 2016, Wiley

    Dr John Mitchell

  32. Drug Design for CNS Diseases: Polypharmacological Profiling of Compounds Using Cheminformatic, 3D-QSAR and Virtual Screening Methodologies

    Article • Frontiers in Neuroscience, June 2016, Frontiers

    Dr John Mitchell

  33. A Random Forest Model for Predicting Allosteric and Functional Sites on Proteins

    Article • Molecular Informatics, January 2016, Wiley

    Dr John Mitchell

  34. Why do Sequence Signatures Predict Enzyme Mechanism? Homology versus Chemistry

    Article • Evolutionary Bioinformatics, December 2015, Libertas Academica, Ltd.

    Dr John Mitchell

  35. Enzyme mechanism prediction: a template matching problem on InterPro signature subspaces

    Article • BMC Research Notes, December 2015, Springer Science + Business Media

    Dr John Mitchell

  36. A note on utilising binary features as ligand descriptors

    Article • Journal of Cheminformatics, December 2015, Springer Science + Business Media

    Dr John Mitchell

  37. The Parzen Window method: In terms of two vectors and one matrix

    Article • Pattern Recognition Letters, October 2015, Elsevier

    Dr John Mitchell

  38. Predicting Melting Points of Organic Molecules: Applications to Aqueous Solubility Prediction Using the General Solubility Equation

    Article • Molecular Informatics, July 2015, Wiley

    Dr John Mitchell

  39. Verifying the fully “Laplacianised” posterior Naïve Bayesian approach and more

    Article • Journal of Cheminformatics, June 2015, Springer Science + Business Media

    Dr John Mitchell

  40. Greedy and Linear Ensembles of Machine Learning Methods Outperform Single Approaches for QSPR Regression Problems

    Article • Molecular Informatics, March 2015, Wiley

    Dr John Mitchell

  41. A review of methods for the calculation of solution free energies and the modelling of systems in solution

    Article • Physical Chemistry Chemical Physics, January 2015, Royal Society of Chemistry

    Dr John Mitchell

  42. Predicting targets of compounds against neurological diseases using cheminformatic methodology

    Article • Journal of Computer-Aided Molecular Design, November 2014, Springer Science + Business Media

    Dr John Mitchell, Dr Rona R. Ramsay

  43. One origin for metallo-β-lactamase activity, or two? An investigation assessing a diverse set of reconstructed ancestral sequences based on a sample of phylogenetic trees

    Article • Journal of Molecular Evolution, September 2014, Springer Science + Business Media

    Dr John Mitchell

  44. Is Experimental Data Quality the Limiting Factor in Predicting the Aqueous Solubility of Druglike Molecules?

    Article • Molecular Pharmaceutics, August 2014, American Chemical Society (ACS)

    Dr John Mitchell, Dr David S Palmer

  45. Erratum for “In Silico Target Predictions: Defining a Benchmarking Data Set and Comparison of Performance of the Multiclass Naı̈ve Bayes and Parzen-Rosenblatt Window”

    Article • Journal of Chemical Information and Modeling, June 2014, American Chemical Society (ACS)

    Dr John Mitchell

  46. The Natural History of Biocatalytic Mechanisms

    Article • PLoS Computational Biology, May 2014, PLOS

    Professor Gustavo Caetano-Anolles, Dr John Mitchell

  47. From sequence to enzyme mechanism using multi-label machine learning

    Article • BMC Bioinformatics, May 2014, Springer Science + Business Media

    Dr John Mitchell

  48. Uniting Cheminformatics and Chemical Theory To Predict the Intrinsic Aqueous Solubility of Crystalline Druglike Molecules

    Article • Journal of Chemical Information and Modeling, March 2014, American Chemical Society (ACS)

    Dr John Mitchell

  49. Machine learning methods in chemoinformatics

    Article • Wiley Interdisciplinary Reviews Computational Molecular Science, February 2014, Wiley

    Dr John Mitchell

  50. PFClust: an optimised implementation of a parameter-free clustering algorithm

    Article • Source Code for Biology and Medicine, January 2014, Springer Science + Business Media

    Dr John Mitchell

  51. Full “Laplacianised” posterior naive Bayesian algorithm

    Article • Journal of Cheminformatics, August 2013, Springer Science + Business Media

    Dr John Mitchell

  52. 4273π: Bioinformatics education on low cost ARM hardware

    Article • BMC Bioinformatics, August 2013, Springer Science + Business Media

    Dr John Mitchell

  53. In Silico Target Predictions: Defining a Benchmarking Data Set and Comparison of Performance of the Multiclass Naïve Bayes and Parzen-Rosenblatt Window

    Article • Journal of Chemical Information and Modeling, July 2013, American Chemical Society (ACS)

    Dr John Mitchell

  54. PFClust: a novel parameter free clustering algorithm

    Article • BMC Bioinformatics, July 2013, Springer Science + Business Media

    Dr John Mitchell

  55. Predicting the protein targets for athletic performance-enhancing substances

    Article • Journal of Cheminformatics, June 2013, Springer Science + Business Media

    Dr John Mitchell

  56. First-Principles Calculation of the Intrinsic Aqueous Solubility of Crystalline Druglike Molecules

    Article • Journal of Chemical Theory and Computation, September 2012, American Chemical Society (ACS)

    Dr John Mitchell, Dr David S Palmer

  57. Enzyme Informatics

    Article • Current Topics in Medicinal Chemistry, September 2012, Bentham Science Publishers

    Dr John Mitchell

  58. Hierarchical virtual screening for the discovery of new molecular scaffolds in antibacterial hit identification

    Article • Journal of The Royal Society Interface, August 2012, Royal Society Publishing

    Dr John Mitchell

  59. Is EC class predictable from reaction mechanism?

    Article • BMC Bioinformatics, April 2012, Springer Science + Business Media

    Dr John Mitchell

  60. Predicting the mechanism of phospholipidosis

    Article • Journal of Cheminformatics, January 2012, Springer Science + Business Media

    Dr John Mitchell

  61. Comments on “Leave-Cluster-Out Cross-Validation Is Appropriate for Scoring Functions Derived from Diverse Protein Data Sets”: Significance for the Validation of Scoring Functions

    Article • Journal of Chemical Information and Modeling, August 2011, American Chemical Society (ACS)

    Dr John Mitchell

  62. Classifying Molecules Using a Sparse Probabilistic Kernel Binary Classifier

    Article • Journal of Chemical Information and Modeling, July 2011, American Chemical Society (ACS)

    Dr John Mitchell

  63. Characterizing the complexity of enzymes on the basis of their mechanisms and structures with a bio-computational analysis

    Article • European Journal of Biochemistry, June 2011, Wiley

    Dr John Mitchell

  64. Development and Comparison of hERG Blocker Classifiers: Assessment on Different Datasets Yields Markedly Different Results

    Article • Molecular Informatics, May 2011, Wiley

    Dr John Mitchell

  65. Informatics, Machine Learning and Computational Medicinal Chemistry

    Article • Future Medicinal Chemistry, March 2011, Taylor & Francis

    Dr John Mitchell

  66. Predicting Phospholipidosis Using Machine Learning

    Article • Molecular Pharmaceutics, October 2010, American Chemical Society (ACS)

    Dr John Mitchell

  67. A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking

    Article • Bioinformatics, March 2010, Oxford University Press (OUP)

    Dr John Mitchell

  68. Quantitative Comparison of Catalytic Mechanisms and Overall Reactions in Convergently Evolved Enzymes: Implications for Classification of Enzyme Function

    Article • PLoS Computational Biology, March 2010, PLOS

    Dr John Mitchell

  69. Understanding the Functional Roles of Amino Acid Residues in Enzyme Catalysis

    Article • Journal of Molecular Biology, July 2009, Elsevier

    Dr John Mitchell

  70. Theoretical Study of the Reaction Mechanism of Streptomyces coelicolor Type II Dehydroquinase

    Article • Journal of Chemical Theory and Computation, May 2009, American Chemical Society (ACS)

    Dr John Mitchell

  71. Computational toxicology: an overview of the sources of data and of modelling methods

    Article • Expert Opinion on Drug Metabolism & Toxicology, January 2009, Informa Healthcare

    Dr John Mitchell

  72. Ligand-Target Prediction Using Winnow and Naive Bayesian Algorithms and the Implications of Overall Performance Statistics

    Article • Journal of Chemical Information and Modeling, December 2008, American Chemical Society (ACS)

    Dr John Mitchell

  73. Simultaneous feature selection and parameter optimisation using an artificial ant colony: case study of melting point prediction

    Article • Chemistry Central Journal, October 2008, Springer Science + Business Media

    Dr John Mitchell, Dr David S Palmer

  74. Toxicological relationships between proteins obtained from protein target predictions of large toxicity databases

    Article • Toxicology and Applied Pharmacology, September 2008, Elsevier

    Dr John Mitchell

  75. Predicting Intrinsic Aqueous Solubility by a Thermodynamic Cycle

    Article • Molecular Pharmaceutics, February 2008, American Chemical Society (ACS)

    Professor Graeme Day, Dr John Mitchell, Dr David S Palmer

  76. A novel hybrid ultrafast shape descriptor method for use in virtual screening

    Article • Chemistry Central Journal, February 2008, Springer Science + Business Media

    Dr John Mitchell

  77. How To Winnow Actives from Inactives:  Introducing Molecular Orthogonal Sparse Bigrams (MOSBs) and Multiclass Winnow

    Article • Journal of Chemical Information and Modeling, February 2008, American Chemical Society (ACS)

    Dr John Mitchell

  78. Why Are Some Properties More Difficult To Predict than Others? A Study of QSPR Models of Solubility, Melting Point, and Log P

    Article • Journal of Chemical Information and Modeling, January 2008, American Chemical Society (ACS)

    Dr John Mitchell, Dr David S Palmer

  79. The Chemistry of Protein Catalysis

    Article • Journal of Molecular Biology, October 2007, Elsevier

    Dr John Mitchell

  80. The Geometry of Interactions between Catalytic Residues and their Substrates

    Article • Journal of Molecular Biology, June 2007, Elsevier

    Dr John Mitchell

  81. Using Reaction Mechanism to Measure Enzyme Similarity

    Article • Journal of Molecular Biology, May 2007, Elsevier

    Dr John Mitchell

  82. Support vector inductive logic programming outperforms the naive Bayes classifier and inductive logic programming for the classification of bioactive chemical compounds

    Article • Journal of Computer-Aided Molecular Design, March 2007, Springer Science + Business Media

    Dr John Mitchell

  83. MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms

    Article • Nucleic Acids Research, January 2007, Oxford University Press (OUP)

    Dr John Mitchell

  84. Article • BMC Bioinformatics, January 2007, Springer Science + Business Media

    Dr John Mitchell

  85. Random Forest Models To Predict Aqueous Solubility

    Article • Journal of Chemical Information and Modeling, January 2007, American Chemical Society (ACS)

    Dr John Mitchell, Dr David S Palmer

  86. Melting Point Prediction Employing k -Nearest Neighbor Algorithms and Genetic Parameter Optimization

    Article • Journal of Chemical Information and Modeling, November 2006, American Chemical Society (ACS)

    Dr John Mitchell

  87. Chemoinformatics-Based Classification of Prohibited Substances Employed for Doping in Sport

    Article • Journal of Chemical Information and Modeling, November 2006, American Chemical Society (ACS)

    Dr John Mitchell, Dr David S Palmer

  88. MACiE: a database of enzyme reaction mechanisms

    Article • Bioinformatics, September 2005, Oxford University Press (OUP)

    Dr John Mitchell

  89. Knowledge Based Potentials: the Reverse Boltzmann Methodology, Virtual Screening and Molecular Weight Dependence

    Article • QSAR & Combinatorial Science, June 2005, Wiley

    Dr John Mitchell

  90. Article • BMC Bioinformatics, January 2005, Springer Science + Business Media

    Dr John Mitchell

  91. Article • BMC Bioinformatics, January 2005, Springer Science + Business Media

    Dr John Mitchell

  92. Predicting protein–ligand binding affinities: a low scoring game?

    Article • Organic & Biomolecular Chemistry, January 2004, Royal Society of Chemistry

    Dr John Mitchell

  93. A structure–odour relationship study using EVA descriptors and hierarchical clustering

    Article • Organic & Biomolecular Chemistry, January 2004, Royal Society of Chemistry

    Dr John Mitchell

  94. Can we predict lattice energy from molecular structure?

    Article • Acta Crystallographica Section B Structural Science, September 2003, International Union of Crystallography

    Dr John Mitchell

  95. Protein Ligand Database (PLD): additional understanding of the nature and specificity of protein-ligand complexes

    Article • Bioinformatics, September 2003, Oxford University Press (OUP)

    Dr John Mitchell

  96. D-amino acid residues in peptides and proteins

    Article • Proteins Structure Function and Bioinformatics, January 2003, Wiley

    Dr John Mitchell

  97. Triazinone tautomers: solid phase energetics

    Article • CrystEngComm, January 2003, Royal Society of Chemistry

    Dr John Mitchell

  98. Anisotropic Repulsion Potentials for Cyanuric Chloride (C 3 N 3 Cl 3 ) and Their Application to Modeling the Crystal Structures of Azaaromatic Chlorides

    Article • The Journal of Physical Chemistry A, November 2001, American Chemical Society (ACS)

    Dr John Mitchell

  99. The Relationship between the Sequence Identities of Alpha Helical Proteins in the PDB and the Molecular Similarities of Their Ligands

    Article • Journal of Chemical Information and Modeling, November 2001, American Chemical Society (ACS)

    Dr John Mitchell

  100. The Determination of the Crystal Structure of Anhydrous Theophylline by X-ray Powder Diffraction with a Systematic Search Algorithm, Lattice Energy Calculations, and 13 C and 15 N Solid-State NMR:  A Question of Polymorphism in a Given Unit Cell

    Article • The Journal of Physical Chemistry B, June 2001, American Chemical Society (ACS)

    Dr John Mitchell

  101. A Systematic Nonempirical Method of Deriving Model Intermolecular Potentials for Organic Molecules:  Application To Amides

    Article • The Journal of Physical Chemistry A, November 2000, American Chemical Society (ACS)

    Dr John Mitchell

  102. Protein folds and functions

    Article • Structure, July 1998, Elsevier

    Dr John Mitchell

  103. Design, synthesis and structure of a zinc finger with an artificial β-turn

    Article • Journal of Molecular Biology, June 1998, Elsevier

    Dr John Mitchell

  104. Non‐randomness in side‐chain packing: the distribution of interplanar angles

    Article • Proteins Structure Function and Bioinformatics, November 1997, Wiley

    Dr John Mitchell

  105. Multiple Solution Conformations of the Integrin-Binding Cyclic Pentapeptide Cyclo(-Ser-d-Leu-Asp-Val-Pro-). Analysis of the (phi,psi) Space Available to Cyclic Pentapeptides

    Article • European Journal of Biochemistry, December 1996, Wiley

    Dr John Mitchell

  106. Modelling the interactions of protein side-chains

    Article • Molecular Engineering, January 1995, Springer Science + Business Media

    Dr John Mitchell

  107. Amino/Aromatic Interactions in Proteins: Is the Evidence Stacked Against Hydrogen Bonding?

    Article • Journal of Molecular Biology, June 1994, Elsevier

    Dr John Mitchell

  108. Towards an understanding of the arginine-aspartate interaction

    Article • Journal of Molecular Biology, July 1992, Elsevier

    Dr John Mitchell