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John Mitchell - Publications

Affiliations: 
1991-2000 University College London, London, United Kingdom 
 2000-2009 Chemistry University of Cambridge, Cambridge, England, United Kingdom 
 2009- Chemistry University of St Andrews, Saint Andrews, Scotland, United Kingdom 
Area:
Computational chemistry, chemoinformatics, bioinformatics
Website:
http://chemistry.st-andrews.ac.uk/staff/jbom/group/
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82 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Shrimpton-Phoenix E, Mitchell J, Bühl M. Computational Insights into the Catalytic Mechanism of Is-PETase: An Enzyme Capable of degrading poly(ethylene) terephthalate. Chemistry (Weinheim An Der Bergstrasse, Germany). PMID 36112344 DOI: 10.1002/chem.202201728  0.749
2022 Mann P, Smith VA, Mitchell JBO, Dobson S. N-strain epidemic model using bond percolation. Physical Review. E. 106: 014304. PMID 35974532 DOI: 10.1103/PhysRevE.106.014304  0.627
2022 Videla Rodriguez EA, Pértille F, Guerrero-Bosagna C, Mitchell JBO, Jensen P, Smith VA. Practical application of a Bayesian network approach to poultry epigenetics and stress. Bmc Bioinformatics. 23: 261. PMID 35778683 DOI: 10.1186/s12859-022-04800-0  0.251
2022 Mann P, Smith VA, Mitchell JBO, Dobson S. Degree correlations in graphs with clique clustering. Physical Review. E. 105: 044314. PMID 35590545 DOI: 10.1103/PhysRevE.105.044314  0.618
2021 Read BJ, Fisher G, Wissett OLR, Machado TFG, Nicholson J, Mitchell JBO, da Silva RG. Allosteric Inhibition of ATP Phosphoribosyltransferase by Protein:Dipeptide and Protein:Protein Interactions. Acs Infectious Diseases. PMID 34928596 DOI: 10.1021/acsinfecdis.1c00539  0.761
2021 Mann P, Smith VA, Mitchell JBO, Dobson S. Symbiotic and antagonistic disease dynamics on networks using bond percolation. Physical Review. E. 104: 024303. PMID 34525561 DOI: 10.1103/PhysRevE.104.024303  0.618
2021 Mann P, Smith VA, Mitchell JBO, Jefferson C, Dobson S. Exact formula for bond percolation on cliques. Physical Review. E. 104: 024304. PMID 34525512 DOI: 10.1103/PhysRevE.104.024304  0.616
2021 Mann P, Smith VA, Mitchell JBO, Dobson S. Two-pathogen model with competition on clustered networks. Physical Review. E. 103: 062308. PMID 34271633 DOI: 10.1103/PhysRevE.103.062308  0.614
2021 Mann P, Smith VA, Mitchell JBO, Dobson S. Cooperative coinfection dynamics on clustered networks. Physical Review. E. 103: 042307. PMID 34005956 DOI: 10.1103/PhysRevE.103.042307  0.612
2021 Fowles DJ, Palmer DS, Guo R, Price SL, Mitchell JBO. Toward Physics-Based Solubility Computation for Pharmaceuticals to Rival Informatics. Journal of Chemical Theory and Computation. PMID 33988381 DOI: 10.1021/acs.jctc.1c00130  0.743
2021 Mann P, Smith VA, Mitchell JBO, Dobson S. Random graphs with arbitrary clustering and their applications. Physical Review. E. 103: 012309. PMID 33601615 DOI: 10.1103/PhysRevE.103.012309  0.621
2021 Mann P, Smith VA, Mitchell JBO, Dobson S. Percolation in random graphs with higher-order clustering. Physical Review. E. 103: 012313. PMID 33601539 DOI: 10.1103/PhysRevE.103.012313  0.62
2020 Mitchell JBO. Three machine learning models for the 2019 Solubility Challenge. Admet & Dmpk. 8: 215-250. PMID 35300305 DOI: 10.5599/admet.835  0.309
2020 Mitchell J. Three machine learning models for the 2019 Solubility Challenge Admet and Dmpk. DOI: 10.5599/Admet.835  0.348
2018 Addicoat M, Adjiman CS, Arhangelskis M, Beran GJO, Bowskill D, Brandenburg JG, Braun DE, Burger V, Cole J, Cruz-Cabeza AJ, Day GM, Deringer VL, Guo R, Hare A, Helfferich J, ... ... Mitchell JBO, et al. Crystal structure evaluation: calculating relative stabilities and other criteria: general discussion. Faraday Discussions. PMID 30302459 DOI: 10.1039/C8Fd90031K  0.635
2018 Burger V, Claeyssens F, Davies DW, Day GM, Dyer MS, Hare A, Li Y, Mellot-Draznieks C, Mitchell JBO, Mohamed S, Oganov AR, Price SL, Ruggiero M, Ryder MR, Sastre G, et al. Applications of crystal structure prediction - inorganic and network structures: general discussion. Faraday Discussions. PMID 30298165 DOI: 10.1039/C8Fd90034E  0.655
2018 Adjiman CS, Brandenburg JG, Braun DE, Cole J, Collins C, Cooper AI, Cruz-Cabeza AJ, Day GM, Dudek M, Hare A, Iuzzolino L, McKay D, Mitchell JBO, Mohamed S, Neelamraju S, et al. Applications of crystal structure prediction - organic molecular structures: general discussion. Faraday Discussions. PMID 30285020 DOI: 10.1039/C8Fd90032A  0.66
2017 Boobier S, Osbourn A, Mitchell JBO. Can human experts predict solubility better than computers? Journal of Cheminformatics. 9: 63. PMID 29238891 DOI: 10.1186/s13321-017-0250-y  0.316
2017 Mitchell JB. Enzyme function and its evolution. Current Opinion in Structural Biology. 47: 151-156. PMID 29107208 DOI: 10.1016/j.sbi.2017.10.004  0.394
2017 Vucicevic J, Nikolic K, Mitchell JBO. Rational drug design of antineoplastic agents using 3D-QSAR, cheminformatic, and virtual screening approaches. Current Medicinal Chemistry. PMID 28707592 DOI: 10.2174/0929867324666170712115411  0.239
2016 McDonagh J, Palmer DS, Van Mourik T, Mitchell JB. Are The Sublimation Thermodynamics of organic molecules predictable? Journal of Chemical Information and Modeling. PMID 27749062 DOI: 10.1021/acs.jcim.6b00033  0.789
2016 Chen AS, Westwood NJ, Brear P, Rogers GW, Mavridis L, Mitchell JB. A Random Forest Model for Predicting Allosteric and Functional Sites on Proteins. Molecular Informatics. 35: 125-35. PMID 27491922 DOI: 10.1002/Minf.201500108  0.789
2016 Nikolic K, Mavridis L, Djikic T, Vucicevic J, Agbaba D, Yelekci K, Mitchell JB. Drug Design for CNS Diseases: Polypharmacological Profiling of Compounds Using Cheminformatic, 3D-QSAR and Virtual Screening Methodologies. Frontiers in Neuroscience. 10: 265. PMID 27375423 DOI: 10.3389/Fnins.2016.00265  0.73
2015 Kew W, Mitchell JB. Greedy and Linear Ensembles of Machine Learning Methods Outperform Single Approaches for QSPR Regression Problems. Molecular Informatics. 34: 634-647. PMID 27490713 DOI: 10.1002/minf.201400122  0.31
2015 Beattie KE, De Ferrari L, Mitchell JB. Why do Sequence Signatures Predict Enzyme Mechanism? Homology versus Chemistry. Evolutionary Bioinformatics Online. 11: 267-74. PMID 26740739 DOI: 10.4137/EBO.S31482  0.391
2015 Mussa HY, De Ferrari L, Mitchell JB. Enzyme mechanism prediction: a template matching problem on InterPro signature subspaces. Bmc Research Notes. 8: 744. PMID 26634450 DOI: 10.1186/s13104-015-1730-7  0.397
2015 Mussa HY, Mitchell JB, Glen RC. A note on utilising binary features as ligand descriptors. Journal of Cheminformatics. 7: 58. PMID 26628925 DOI: 10.1186/S13321-015-0105-3  0.315
2015 Mussa HY, Mitchell JB, Afzal AM. The Parzen Window method: In terms of two vectors and one matrix. Pattern Recognition Letters. 63: 30-35. PMID 26435560 DOI: 10.1016/j.patrec.2015.06.002  0.266
2015 Mussa HY, Marcus D, Mitchell JB, Glen RC. Verifying the fully "Laplacianised" posterior Naïve Bayesian approach and more. Journal of Cheminformatics. 7: 27. PMID 26075027 DOI: 10.1186/S13321-015-0075-5  0.278
2015 Nikolic K, Mavridis L, Bautista-Aguilera OM, Marco-Contelles J, Stark H, do Carmo Carreiras M, Rossi I, Massarelli P, Agbaba D, Ramsay RR, Mitchell JB. Predicting targets of compounds against neurological diseases using cheminformatic methodology. Journal of Computer-Aided Molecular Design. 29: 183-98. PMID 25425329 DOI: 10.1007/S10822-014-9816-1  0.73
2014 Alderson RG, Barker D, Mitchell JB. 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. Journal of Molecular Evolution. 79: 117-29. PMID 25185655 DOI: 10.1007/s00239-014-9639-7  0.76
2014 Palmer DS, Mitchell JB. Is experimental data quality the limiting factor in predicting the aqueous solubility of druglike molecules? Molecular Pharmaceutics. 11: 2962-72. PMID 24919008 DOI: 10.1021/mp500103r  0.544
2014 De Ferrari L, Mitchell JB. From sequence to enzyme mechanism using multi-label machine learning. Bmc Bioinformatics. 15: 150. PMID 24885296 DOI: 10.1186/1471-2105-15-150  0.448
2014 Nath N, Mitchell JB, Caetano-Anollés G. The natural history of biocatalytic mechanisms. Plos Computational Biology. 10: e1003642. PMID 24874434 DOI: 10.1371/Journal.Pcbi.1003642  0.747
2014 McDonagh JL, Nath N, De Ferrari L, van Mourik T, Mitchell JB. Uniting cheminformatics and chemical theory to predict the intrinsic aqueous solubility of crystalline druglike molecules. Journal of Chemical Information and Modeling. 54: 844-56. PMID 24564264 DOI: 10.1021/Ci4005805  0.777
2014 Musayeva K, Henderson T, Mitchell JB, Mavridis L. PFClust: an optimised implementation of a parameter-free clustering algorithm. Source Code For Biology and Medicine. 9: 5. PMID 24490618 DOI: 10.1186/1751-0473-9-5  0.711
2013 Mussa HY, Mitchell JB, Glen RC. Full "Laplacianised" posterior naive Bayesian algorithm. Journal of Cheminformatics. 5: 37. PMID 23968281 DOI: 10.1186/1758-2946-5-37  0.257
2013 Koutsoukas A, Lowe R, Kalantarmotamedi Y, Mussa HY, Klaffke W, Mitchell JB, Glen RC, Bender A. In silico target predictions: defining a benchmarking data set and comparison of performance of the multiclass Naïve Bayes and Parzen-Rosenblatt window. Journal of Chemical Information and Modeling. 53: 1957-66. PMID 23829430 DOI: 10.1021/Ci300435J  0.568
2013 Mavridis L, Nath N, Mitchell JB. PFClust: a novel parameter free clustering algorithm. Bmc Bioinformatics. 14: 213. PMID 23819480 DOI: 10.1186/1471-2105-14-213  0.753
2013 Mavridis L, Mitchell JB. Predicting the protein targets for athletic performance-enhancing substances. Journal of Cheminformatics. 5: 31. PMID 23800040 DOI: 10.1186/1758-2946-5-31  0.738
2012 Palmer DS, McDonagh JL, Mitchell JB, van Mourik T, Fedorov MV. First-Principles Calculation of the Intrinsic Aqueous Solubility of Crystalline Druglike Molecules. Journal of Chemical Theory and Computation. 8: 3322-3337. PMID 26605739 DOI: 10.1021/ct300345m  0.774
2012 Alderson RG, De Ferrari L, Mavridis L, McDonagh JL, Mitchell JB, Nath N. Enzyme informatics. Current Topics in Medicinal Chemistry. 12: 1911-23. PMID 23116471 DOI: 10.2174/156802612804547353  0.76
2012 Ballester PJ, Mangold M, Howard NI, Robinson RL, Abell C, Blumberger J, Mitchell JB. Hierarchical virtual screening for the discovery of new molecular scaffolds in antibacterial hit identification. Journal of the Royal Society, Interface / the Royal Society. 9: 3196-207. PMID 22933186 DOI: 10.1098/Rsif.2012.0569  0.527
2012 Nath N, Mitchell JB. Is EC class predictable from reaction mechanism? Bmc Bioinformatics. 13: 60. PMID 22530800 DOI: 10.1186/1471-2105-13-60  0.746
2012 Lowe R, Mussa HY, Nigsch F, Glen RC, Mitchell JB. Predicting the mechanism of phospholipidosis. Journal of Cheminformatics. 4: 2. PMID 22281160 DOI: 10.1186/1758-2946-4-2  0.737
2011 Marchese Robinson RL, Glen RC, Mitchell JB. Development and Comparison of hERG Blocker Classifiers: Assessment on Different Datasets Yields Markedly Different Results. Molecular Informatics. 30: 443-58. PMID 27467090 DOI: 10.1002/Minf.201000159  0.325
2011 Bajorath J, Barreca ML, Bender A, Bryce R, Hutter M, Laggner C, Laughton C, Martin Y, Mitchell J, Padova A, Renner S, Selzer PM, Sherman W, Sippl W, Taft C, et al. Ask the experts: focus on computational chemistry. Future Medicinal Chemistry. 3: 909-921. PMID 21707395 DOI: 10.4155/Fmc.11.57  0.377
2011 Lowe R, Mussa HY, Mitchell JB, Glen RC. Classifying molecules using a sparse probabilistic kernel binary classifier. Journal of Chemical Information and Modeling. 51: 1539-44. PMID 21696153 DOI: 10.1021/Ci200128W  0.527
2011 Holliday GL, Fischer JD, Mitchell JB, Thornton JM. Characterizing the complexity of enzymes on the basis of their mechanisms and structures with a bio-computational analysis. The Febs Journal. 278: 3835-45. PMID 21605342 DOI: 10.1111/J.1742-4658.2011.08190.X  0.761
2011 Ballester PJ, Mitchell JB. 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. Journal of Chemical Information and Modeling. 51: 1739-41. PMID 21591735 DOI: 10.1021/ci200057e  0.539
2011 Mitchell JB. Informatics, machine learning and computational medicinal chemistry. Future Medicinal Chemistry. 3: 451-67. PMID 21452981 DOI: 10.4155/fmc.11.11  0.312
2011 Marchese Robinson RL, Glen RC, Mitchell JBO. Development and comparison of herg blocker classifiers: Assessment on different datasets yields markedly different results Molecular Informatics. 30: 443-458. DOI: 10.1002/minf.201000159  0.247
2010 Lowe R, Glen RC, Mitchell JB. Predicting phospholipidosis using machine learning. Molecular Pharmaceutics. 7: 1708-14. PMID 20799726 DOI: 10.1021/Mp100103E  0.537
2010 Almonacid DE, Yera ER, Mitchell JB, Babbitt PC. Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function. Plos Computational Biology. 6: e1000700. PMID 20300652 DOI: 10.1371/Journal.Pcbi.1000700  0.755
2010 Ballester PJ, Mitchell JB. A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking. Bioinformatics (Oxford, England). 26: 1169-75. PMID 20236947 DOI: 10.1093/bioinformatics/btq112  0.59
2009 Blomberg LM, Mangold M, Mitchell JB, Blumberger J. Theoretical Study of the Reaction Mechanism of Streptomyces coelicolor Type II Dehydroquinase. Journal of Chemical Theory and Computation. 5: 1284-94. PMID 26609719 DOI: 10.1021/ct800480d  0.345
2009 Holliday GL, Mitchell JB, Thornton JM. Understanding the functional roles of amino acid residues in enzyme catalysis. Journal of Molecular Biology. 390: 560-77. PMID 19447117 DOI: 10.1016/J.Jmb.2009.05.015  0.729
2009 Nigsch F, Macaluso NJ, Mitchell JB, Zmuidinavicius D. Computational toxicology: an overview of the sources of data and of modelling methods. Expert Opinion On Drug Metabolism & Toxicology. 5: 1-14. PMID 19236225 DOI: 10.1517/17425250802660467  0.654
2008 Nigsch F, Bender A, Jenkins JL, Mitchell JB. Ligand-target prediction using Winnow and naive Bayesian algorithms and the implications of overall performance statistics. Journal of Chemical Information and Modeling. 48: 2313-25. PMID 19055411 DOI: 10.1021/Ci800079X  0.696
2008 O'Boyle NM, Palmer DS, Nigsch F, Mitchell JB. Simultaneous feature selection and parameter optimisation using an artificial ant colony: case study of melting point prediction. Chemistry Central Journal. 2: 21. PMID 18959785 DOI: 10.1186/1752-153X-2-21  0.774
2008 Nigsch F, Mitchell JB. Toxicological relationships between proteins obtained from protein target predictions of large toxicity databases. Toxicology and Applied Pharmacology. 231: 225-34. PMID 18589467 DOI: 10.1016/J.Taap.2008.05.007  0.704
2008 Palmer DS, Llinàs A, Morao I, Day GM, Goodman JM, Glen RC, Mitchell JB. Predicting intrinsic aqueous solubility by a thermodynamic cycle. Molecular Pharmaceutics. 5: 266-79. PMID 18290628 DOI: 10.1021/Mp7000878  0.693
2008 Cannon EO, Nigsch F, Mitchell JB. A novel hybrid ultrafast shape descriptor method for use in virtual screening. Chemistry Central Journal. 2: 3. PMID 18282294 DOI: 10.1186/1752-153X-2-3  0.659
2008 Nigsch F, Mitchell JB. How to winnow actives from inactives: introducing molecular orthogonal sparse bigrams (MOSBs) and multiclass Winnow. Journal of Chemical Information and Modeling. 48: 306-18. PMID 18220378 DOI: 10.1021/Ci700350N  0.686
2008 Hughes LD, Palmer DS, Nigsch F, Mitchell JB. Why are some properties more difficult to predict than others? A study of QSPR models of solubility, melting point, and Log P. Journal of Chemical Information and Modeling. 48: 220-32. PMID 18186622 DOI: 10.1021/Ci700307P  0.744
2007 Holliday GL, Almonacid DE, Mitchell JB, Thornton JM. The chemistry of protein catalysis. Journal of Molecular Biology. 372: 1261-77. PMID 17727879 DOI: 10.1016/J.Jmb.2007.07.034  0.798
2007 Torrance JW, Holliday GL, Mitchell JB, Thornton JM. The geometry of interactions between catalytic residues and their substrates. Journal of Molecular Biology. 369: 1140-52. PMID 17466330 DOI: 10.1016/J.Jmb.2007.03.055  0.771
2007 O'Boyle NM, Holliday GL, Almonacid DE, Mitchell JB. Using reaction mechanism to measure enzyme similarity. Journal of Molecular Biology. 368: 1484-99. PMID 17400244 DOI: 10.1016/j.jmb.2007.02.065  0.786
2007 Cannon EO, Amini A, Bender A, Sternberg MJ, Muggleton SH, Glen RC, Mitchell JB. Support vector inductive logic programming outperforms the naive Bayes classifier and inductive logic programming for the classification of bioactive chemical compounds. Journal of Computer-Aided Molecular Design. 21: 269-80. PMID 17387437 DOI: 10.1007/S10822-007-9113-3  0.321
2007 Konstantinou-Kirtay C, Mitchell JB, Lumley JA. Scoring functions and enrichment: a case study on Hsp90. Bmc Bioinformatics. 8: 27. PMID 17257425 DOI: 10.1186/1471-2105-8-27  0.274
2007 Palmer DS, O'Boyle NM, Glen RC, Mitchell JB. Random forest models to predict aqueous solubility. Journal of Chemical Information and Modeling. 47: 150-8. PMID 17238260 DOI: 10.1021/Ci060164K  0.763
2007 Holliday GL, Almonacid DE, Bartlett GJ, O'Boyle NM, Torrance JW, Murray-Rust P, Mitchell JB, Thornton JM. MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms. Nucleic Acids Research. 35: D515-20. PMID 17082206 DOI: 10.1093/Nar/Gkl774  0.785
2006 Nigsch F, Bender A, van Buuren B, Tissen J, Nigsch E, Mitchell JB. Melting point prediction employing k-nearest neighbor algorithms and genetic parameter optimization. Journal of Chemical Information and Modeling. 46: 2412-22. PMID 17125183 DOI: 10.1021/Ci060149F  0.69
2006 Cannon EO, Bender A, Palmer DS, Mitchell JB. Chemoinformatics-based classification of prohibited substances employed for doping in sport. Journal of Chemical Information and Modeling. 46: 2369-80. PMID 17125180 DOI: 10.1021/Ci0601160  0.538
2005 Holliday GL, Bartlett GJ, Almonacid DE, O'Boyle NM, Murray-Rust P, Thornton JM, Mitchell JB. MACiE: a database of enzyme reaction mechanisms. Bioinformatics (Oxford, England). 21: 4315-6. PMID 16188925 DOI: 10.1093/Bioinformatics/Bti693  0.786
2005 Murray-Rust P, Mitchell JB, Rzepa HS. Communication and re-use of chemical information in bioscience. Bmc Bioinformatics. 6: 180. PMID 16026614 DOI: 10.1186/1471-2105-6-180  0.284
2005 Murray-Rust P, Mitchell JB, Rzepa HS. Chemistry in bioinformatics. Bmc Bioinformatics. 6: 141. PMID 15941476 DOI: 10.1186/1471-2105-6-141  0.257
2004 Marsden PM, Puvanendrampillai D, Mitchell JB, Glen RC. Predicting protein-ligand binding affinities: a low scoring game? Organic & Biomolecular Chemistry. 2: 3267-73. PMID 15534704 DOI: 10.1039/B409570G  0.76
2004 Takane SY, Mitchell JB. A structure-odour relationship study using EVA descriptors and hierarchical clustering. Organic & Biomolecular Chemistry. 2: 3250-5. PMID 15534702 DOI: 10.1039/B409802A  0.259
2003 Ouvrard C, Mitchell JB. Can we predict lattice energy from molecular structure? Acta Crystallographica. Section B, Structural Science. 59: 676-85. PMID 14586090  0.303
2003 Puvanendrampillai D, Mitchell JB. L/D Protein Ligand Database (PLD): additional understanding of the nature and specificity of protein-ligand complexes. Bioinformatics (Oxford, England). 19: 1856-7. PMID 14512362 DOI: 10.1093/Bioinformatics/Btg243  0.754
2003 Mitchell JB, Smith J. D-amino acid residues in peptides and proteins. Proteins. 50: 563-71. PMID 12577262 DOI: 10.1002/prot.10320  0.257
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