All Stories

  1. 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

  2. Artificial intelligence in pharmaceutical research and development

    Article • Future Medicinal Chemistry, July 2018, Future Science

    Dr John Mitchell

  3. 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

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

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

    Dr John Mitchell, Marta Dudek

  5. 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

  6. Can human experts predict solubility better than computers?

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

    Dr John Mitchell

  7. Enzyme function and its evolution

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

    Dr John Mitchell

  8. 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

  9. Are the Sublimation Thermodynamics of Organic Molecules Predictable?

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

    Dr John Mitchell

  10. 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

  11. 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

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

    Article • Molecular Informatics, January 2016, Wiley

    Dr John Mitchell

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

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

    Dr John Mitchell

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

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

    Dr John Mitchell

  15. A note on utilising binary features as ligand descriptors

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

    Dr John Mitchell

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

    Article • Pattern Recognition Letters, October 2015, Elsevier

    Dr John Mitchell

  17. 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

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

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

    Dr John Mitchell

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

    Article • Molecular Informatics, March 2015, Wiley

    Dr John Mitchell

  20. 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

  21. 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

  22. 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

  23. 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

  24. 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

  25. The Natural History of Biocatalytic Mechanisms

    Article • PLoS Computational Biology, May 2014, PLOS

    Professor Gustavo Caetano-Anolles, Dr John Mitchell

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

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

    Dr John Mitchell

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

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

    Dr John Mitchell

  28. Machine learning methods in chemoinformatics

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

    Dr John Mitchell

  29. 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

  30. Full “Laplacianised” posterior naive Bayesian algorithm

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

    Dr John Mitchell

  31. 4273π: Bioinformatics education on low cost ARM hardware

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

    Dr John Mitchell

  32. 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

  33. PFClust: a novel parameter free clustering algorithm

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

    Dr John Mitchell

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

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

    Dr John Mitchell

  35. 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

  36. Enzyme Informatics

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

    Dr John Mitchell

  37. 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

  38. Is EC class predictable from reaction mechanism?

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

    Dr John Mitchell

  39. Predicting the mechanism of phospholipidosis

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

    Dr John Mitchell

  40. 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 Computer Sciences, August 2011, American Chemical Society (ACS)

    Dr John Mitchell

  41. Classifying Molecules Using a Sparse Probabilistic Kernel Binary Classifier

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

    Dr John Mitchell

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

    Article • FEBS Journal, June 2011, Wiley

    Dr John Mitchell

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

    Article • Molecular Informatics, May 2011, Wiley

    Dr John Mitchell

  44. Informatics, machine learning and computational medicinal chemistry

    Article • Future Medicinal Chemistry, March 2011, Future Science

    Dr John Mitchell

  45. Predicting Phospholipidosis Using Machine Learning

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

    Dr John Mitchell

  46. 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

  47. 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

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

    Article • Journal of Molecular Biology, July 2009, Elsevier

    Dr John Mitchell

  49. 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

  50. 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

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

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

    Dr John Mitchell

  52. 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

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

    Article • Toxicology and Applied Pharmacology, September 2008, Elsevier

    Dr John Mitchell

  54. 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

  55. 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

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

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

    Dr John Mitchell

  57. 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 Computer Sciences, January 2008, American Chemical Society (ACS)

    Dr John Mitchell, Dr David S Palmer

  58. The Chemistry of Protein Catalysis

    Article • Journal of Molecular Biology, October 2007, Elsevier

    Dr John Mitchell

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

    Article • Journal of Molecular Biology, June 2007, Elsevier

    Dr John Mitchell

  60. Using Reaction Mechanism to Measure Enzyme Similarity

    Article • Journal of Molecular Biology, May 2007, Elsevier

    Dr John Mitchell

  61. 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

  62. 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

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

    Dr John Mitchell

  64. Random Forest Models To Predict Aqueous Solubility

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

    Dr John Mitchell, Dr David S Palmer

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

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

    Dr John Mitchell

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

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

    Dr John Mitchell, Dr David S Palmer

  67. MACiE: a database of enzyme reaction mechanisms

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

    Dr John Mitchell

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

    Article • QSAR & Combinatorial Science, June 2005, Wiley

    Dr John Mitchell

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

    Dr John Mitchell

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

    Dr John Mitchell

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

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

    Dr John Mitchell

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

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

    Dr John Mitchell

  73. Can we predict lattice energy from molecular structure?

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

    Dr John Mitchell

  74. 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

  75. D-amino acid residues in peptides and proteins

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

    Dr John Mitchell

  76. Triazinone tautomers: solid phase energetics

    Article • CrystEngComm, January 2003, Royal Society of Chemistry

    Dr John Mitchell

  77. 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

  78. 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 Computer Sciences, November 2001, American Chemical Society (ACS)

    Dr John Mitchell

  79. 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, June 2001, American Chemical Society (ACS)

    Dr John Mitchell

  80. 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

  81. Protein folds and functions

    Article • Structure, July 1998, Elsevier

    Dr John Mitchell

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

    Article • Journal of Molecular Biology, June 1998, Elsevier

    Dr John Mitchell

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

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

    Dr John Mitchell

  84. 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

  85. Modelling the interactions of protein side-chains

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

    Dr John Mitchell

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

    Article • Journal of Molecular Biology, June 1994, Elsevier

    Dr John Mitchell

  87. Towards an understanding of the arginine-aspartate interaction

    Article • Journal of Molecular Biology, July 1992, Elsevier

    Dr John Mitchell