Centre for Molecular Design (CMD)

Publications: Papers 2000 - 2009


  • C. Kormann, I. Pimenta, S. Löber, C. Wimmer, H. Lanig, T. Clark, W. Hillen and P. Gmeiner
    Diarylpropane-1,3-dione derivatives as TetR-Inducing Tetracycline Mimetics: Synthesis and Biological Investigations
    ChemBioChem, 10, 2924-2933, 2009.

  • A. Molina-Ontoria, G. Fernandez, M. Wielopolski, C. Atienza, L. Sanchez, A. Gouloumis, T. Clark, N. Martin and D. M. Guldi
    Self-Association and Electron Transfer in Donor-Acceptor Dyads Connected by meta-Substituted Oligomers
    J. Am. Chem. Soc., 131, 12218-12229, 2009.

  • C. M. Jäger, A. Hirsch, B. Schade, C. Böttcher and T. Clark
    Counterions Control the Self-Assembly of Structurally Persistent Micelles; Theoretical Prediction and Experimental Observation of Stabilization by Sodium Ions
    Chemistry - A European Journal, 15, 8586-8592, 2009.

  • C. Kramer, T. Heinisch, T. Fligge, B. Beck, and T. Clark
    A Consistent Kinetic Solubility Dataset for Early-phase Drug Discovery
    ChemMedChem, 4, 1529-1536, 2009.

  • F. Haberl, H. Lanig and T. Clark
    Induction of the Tetracycline Repressor: Characterization by Molecular-Dynamics Simulations
    PROTEINS: Structure, Function, and Bioinformatics, 77, 857-866, 2009.

  • H. Kayi and T. Clark
    AM1* parameters for vanadium and chromium
    J. Mol. Model., 15, 1253-1269, 2009.

  • J. S. Murray, A. Toro-Labbé, T. Clark and P. Politzer
    Analysis of diatomic bond dissociation and formation in terms of the reaction force and the position-dependent reaction force constant
    J. Mol. Model., 15, 701-706, 2009.

  • Y. Tanrikulu, E. Proschak, T. Werner, T. Geppert, N. Todoroff, A. Klenner, T. Kottke, K. Sander, E. Schneider, R. Seifert, H. Stark, T. Clark and G. Schneider
    Homology-model adjustment and ligand screening with a pseudoreceptor of human histamine H4 receptor
    ChemMedChem, 4, 820-827, 2009.

  • M. Hennemann, A. Friedl, M. Lobell, J. Keldenich, A. Hillisch, T. Clark and A. H. Göller
    CypScore: Quantitative Prediction of Reactivity toward Cytochromes P450 Based on Semiempirical Molecular Orbital Theory
    ChemMedChem, 4, 657-669, 2009.

  • C. M. Jäger, M. Hennemann and T. Clark
    The Effect of Complexed Lithium Cation on a Norcarane-Based Radical Clock
    Chemistry - A European Journal, 15, 2425-2433, 2009.

  • C. Kramer, C. S. Tautermann, C. Kramer, D. J. Livingstone, D. W. Salt, D. C. Whitley, B. Beck and T. Clark
    Sharpening the toolbox of computational chemistry: A new approximation of critical F-values for multiple linear regression
    J Chem Inf Model., 49, 28-34, 2009.

  • H. Kayi and T. Clark
    AM1* parameters for bromine and iodine
    J. Mol. Model., 15, 295-308, 2009.

  • A. McGready, A. Stevens, M.Lipkin, B. D. Hudson, D. C. Whitley and M. G. Ford
    Vicinity Analysis: a methodology for the identification of similar protein active sites
    J. Mol. Model., 15, 489-498, 2009.

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  • F. Haberl, O. Othersen, U. Seidel, H. Lanig and T. Clark
    Investigating protein-protein and protein-ligand interactions by molecular dynamics simulations
    in High Performance Computing in Science and Engineering, Garching/Munich 2007
    S. Wagner, M. Steinmetz, A. Bode and M. Brehm, (Eds.), Springer, Heidelberg, 2008, pp 153-164.

  • T. E. Shubina and T. Clark
    Redox catalysis and reactivity of metalloporphyrines
    in High Performance Computing in Science and Engineering, Garching/Munich 2007. Transactions of the Third Joint HLRB and KONWIHR Status and Result Workshop, Dec. 3-4, 2007, Leibniz Supercomputing Centre, Garching/Munich, Germany.
    S. Wagner, M. Steinmetz, A. Bode and M. Brehm, (Eds.), Springer, Heidelberg, 2008, pp 201-214.

  • R. Puchta, L. Dahlenburg and T. Clark
    Why do cationic hydridoiridium(III) complexes with β-aminophosphane ligands favour the transfer hydrogenation of ketones over the direct H2-hydrogenation? - A computational approach
    Chemistry - A European Journal,14, 8898-8903, 2008.

  • D. J. Livingstone, T. Clark, M. G. Ford, B. D. Hudson and D. C . Whitley
    QSAR studies using the ParaShift system
    SAR and QSAR in Environmental Research, 19, 285-302, 2008.

  • D. A. Yalalov, S. B. Tsogoeva, T. E. Shubina, I. M. Martynova, T. Clark
    Evidence for an enol mechanism in a highly enantioselective Mannich-type reaction catalyzed by primary amine-thiourea
    Angew. Chem., 120, 6726-6730, 2008.

  • T. Waters, J. Boulton, T. Clark, M. J. Gallen, C. M. Williams and R. A. J. OHair
    Experimental determination of the gas phase proton affinities of the periodinane anions IBX and IBA
    Org. Biomol. Chem., 6, 2530-2533, 2008.

  • B. D. Hudson, D. C. Whitley, M. G. Ford, M. Swain and J. W. Essex
    Pattern recognition based on colour-coded quantum mechanical surfaces for molecular alignment
    J. Mol. Model., 14, 49-57, 2008.

  • D. J. Livingstone, A. Browne, R. Crichton, B. D. Hudson, D. C. Whitley and M. G. Ford
    The extraction of information and knowledge from trained neural networks
    in Artificial Neural Networks: Methods and Applications (Methods in Molecular Biology, vol 458)
    D. J. Livingstone (Ed.), Humana Press, 2008, pp 231-248.

  • S.J. Ajmani, S.C. Rogers, M.H. Barley, A.N. Burgess and D.J. Livingstone
    Characterization of Mixtures Part 1: Prediction of infinite-dilution activity coefficients using neural network-based QSPR models
    QSAR Comb. Sci., 27, 1346-1361, 2008.

  • M. J. Lipkin, A. P. Stevens, D. J. Livingstone and C. J. Harris
    How large does a compound screening collection need to be
    Comb. Chem. High Throughput Screen, 11, 482-493, 2008.

  • D. J. Livingstone and H. van de Waterbeemd
    In Silico Prediction of Human Bioavailability
    in Drug Bioavailability: Estimation of Solubility, Permeability, Absorption and Bioavailability
    H. van de Waterbeemd and B. Testa (Eds.), Wiley-VCH, 2008, pp 433-452.

  • X. Rong, P. Winget and T. Clark
    The cyclooligomerisation of acetylene at metal centres
    Eur. J. Inorg. Chem., 2874-2883, 2008.

  • M. Wielopolski, C. Atienza, T. Clark, D. M.Guldi and N. Martin
    p-Phenyleneethynylene molecular wires: influence of structure on photoinduced electron-transfer properties
    Chem. Eur. J., 14, 6379-6390, 2008.

  • T. Clark, K. G. Byler, and M. J. de Groot
    Biological communication via molecular surfaces
    in Molecular Interactions - Bringing Chemistry to Life, Proceedings of the International Beilstein Workshop, Bozen, Italy, May 15-19, 2006
    Logos Verlag, Berlin, 2008, pp 129-146.
    Available online.

  • M. Hofmann, T. Clark, F. W. Heinemann, and U. Zenneck
    Rock around the ring: an experimental and theoretical study of the molecular dynamics of stannyltriphospholes with chiral tin substituents
    Eur. J. Inorg. Chem., 2225-2237, 2008.

  • A.-J. Jakobi, H. Mauser and T Clark
    ParaFrag - An approach for surface-based similarity comparison of molecular fragments
    J. Mol. Model., 14, 547-558, 2008.

  • C. Jaeger, M. Hennemann, A. Mieszala and T Clark
    An ab initio and density-functional theory study of radical-clock reactions
    J. Org. Chem., 73, 1536-1545, 2008.

  • C. Rusu, H. Lanig, T. Clark and C. Kryschi
    Monitoring biological membrane-potential changes: a CI QM/MM study
    J. Phys. Chem. B, 112, 2445-2455, 2008.

  • C. Kramer, B. Beck, J. M. Kriegl and T. Clark
    A composite model for hERG blockade
    ChemMedChem, 3, 254-265, 2008.

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  • D.W. Salt, S. J. Ajmani, R. Crichton and D.J. Livingstone
    An improved approximation to the estimation of the critical F values in best subset regression
    J. Chem. Inf. Model., 47, 143-149, 2007.

  • L. Mavridis, B. D. Hudson and D. W. Ritchie
    Toward high throughput virtual screening using spherical harmonic surface representations
    J. Chem. Inf. Model., 47, 1787-1796, 2007.

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  • R. Gledhill, S. Kent, B. Hudson, W. G. Richards, J. W. Essex and J. G. Frey
    A computer-aided drug discovery system for chemistry teaching
    J. Chem. Inf. Model., 46, 960-970, 2006.

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  • B. D. Hudson, D. C. Whitley, A. Browne and M. G. Ford
    Extraction of comprehensible rules from neural networks. Application of TREPAN in bio and chemoinformatics
    Croatica Chemica Acta, 78, 557-561, 2005.

  • D.J. Livingstone and D.W. Salt
    Variable Selection - Spoilt for Choice?
    In Reviews in Computational Chemistry, Volume 21 (eds K. B. Lipkowitz, R. Larter and T. R. Cundari), John Wiley & Sons, Inc., Hoboken, NJ, USA.

  • D.J. Livingstone and D.W. Salt
    Judging the significance of multiple linear regression models
    J. Med. Chem., 48, 661-663, 2005.

  • D.W. Salt, B. D. Hudson, L. Banting, M. J. Ellis and M. G. Ford
    Dash: A model analysis method for molecular dynamics simulation data: Analysis of ligands of ppar-γ 
    J. Med. Chem., 48, 3214-3220, 2005.

  • Virtual computational chemistry laboratory - design and description
    J. Comput. Aid. Mol. Des., 19, 453-463, 2005.

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  • A. Browne, B. D. Hudson, D.C. Whitley, M. G. Ford and P. Picton
    Biological data mining with neural networks: implementation and application of a flexible decision tree extraction algorithm to genomic domain problems
    Neurocomputing, 57, 275-293, 2004.

  • A. Browne, B. Hudson, D. Whitley and M. Ford
    Neural networks for knowledge discovery from bioinformatic and cheminformatic datasets
    Proceedings of the Fifth International Conference on Recent Advances in Soft Computing (RASC 2004), Nottingham, UK, pp. 74-79.
    ISBN: 1-84233-110-8.

  • M. Cronin and D.J. Livingstone
    Calculation of Physicochemical Properties
    In Modelling Environmental Fate and Toxicity, M. Cronin and D.J. Livingstone (Eds.)
    Taylor & Francis, London, 2004.
    ISBN: 0-415-27180-0

  • D.J. Livingstone
    Building QSAR Models - A Practical Guide
    In Modelling Environmental Fate and Toxicity, M. Cronin and D.J. Livingstone (Eds.)
    Taylor & Francis, London, 2004.
    ISBN: 0-415-27180-0

  • D.W.Salt, L. Maccari, M.Botta and M.G. Ford
    Variable selection and specification of robust QSAR models from multicollinear data: arylpiperazinyl derivatives with affinity and selectivity for a2-adrenoceptors.
    J. Comp.-Aided Mol. Des., 18, 495-509, 2004.

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  • C. S. Cundy and P. A. Cox
    The hydrothermal synthesis of zeolites: History and development from the earliest days to the present time
    Chemical Reviews, 103, 663-701, 2003.

  • R. Garcia, I. J. Shannon, A. M. Z. Slawin, W. Z. Zhou, P. A. Cox and P. A. Wright
    Synthesis, structure and thermal transformations of aluminophosphates containing the nickel complex [Ni(diethylenetriamine)2]2+ as a structure directing agent
    Microporous and Mesoporous Materials, 58, 91-104, 2003.

  • R. Garcia, T. D. Coombs, I. J. Shannon, P. A. Wright and P. A. Cox
    Nickel amine complexes as structure-directing agents for aluminophosphate molecular sieves: a new route to supported nickel catalysts
    Topics in Catalysis, 24, 115-124, 2003.

  • H. J. Lewerenz, M. Aggour, C. Murrell, M. Kanis, H. Jungblut, J. Jakubowicz, P. A. Cox, S. A. Campbell, P. Hoffmann and D. Schmeisser
    Initial stages of structure formation on silicon electrodes investigated by photoelectron spectroscopy using synchroton radiation and in situ atomic force microscopy
    Journal of the Electrochemical Society, 150, E185-E189, 2003.

  • H. J. Lewerenz, M. Aggour, C. Murrell, J. Jakubowicz, M. Kanis, S. A. Campbell, P. A. Cox, P. Hoffmann, H. Jungblut and D. Schmeisser
    High resolution surface analysis of Si roughening in dilute ammonium flouride solution
    Journal of Electroanalytical Chemistry, 549, 3-6, 2003.

  • D. J. Livingstone
    Theoretical property predictions
    Curr. Top. Med. Chem., 3, 1171-92, 2003.

  • D. J. Livingstone and D. T. Manallack
    Neural networks in 3D QSAR
    QSAR Comb. Sci., 22, 510-18, 2003.

  • D. T. Manallack, B. G. Tehan, E. Garcia, B. D. Hudson, M. G. Ford, D. J. Livingstone, D. C. Whitley and W. R. Pitt
    A concensus neural network-based technique for discriminating soluble and poorly soluble compounds
    J. Chem. Inf. Comput. Sci., 43, 674-679, 2003.

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  • F. J. Carver, C. A. Hunter, D. J. Livingstone, J. F. McCabe and E. M. Seward
    Substituent effects on edge-to-face aromatic interactions
    Chemistry, 8(13), 2848-59, 2002.

  • S. J. Cox, D. W. Salt, B. E. Lee and M. G. Ford
    Modelling the capture of spray droplets by barley
    Wind and Structures, 5, 127-140, 2002.

  • M. Edgar, V. J. Carter, P. Grewal, L. J. Sawers, E. Sastre, D. P. Tunstall, P. A. Cox, P. Lightfoot and P. A. Wright
    Structure elucidation of a novel aluminum methylphosphonate, Al3(CH3PO3)2.O.(OH)3, through a combination of X-ray powder diffraction, solid-state NMR spectroscopy, and computational energy minimization
    Chemistry of Materials, 14, 3432-3439, 2002.

  • M. Edgar, V. J. Carter, G. P. Tunstall, P. Grewal, V. Favre-Nicolin, P. A. Cox, P. Lightfoot and P. A. Wright
    Structure solution of a novel aluminum methylphosphonate using a new simulated annealing program and powder X-ray diffraction data
    Chemical Communications, 8, 808-809, 2002.

  • M. G. Ford, N. E. Hoare, B. D. Hudson, T. G. Nevell and L. Banting
    QSAR studies of the pyrethroid insecticides. Part 3. A putative pharmacophore derived using methodology based on molecular dynamics and hierarchical cluster analysis
    J Mol Graph Model, 21(1), 29-36, 2002.

  • M. Hinaje, M. Ford, L. Banting, S. Arkle and B. Khambay
    An investigation of the ionophoric characteristics of destruxin A
    Arch Biochem Biophys, 405(1), 73-77, 2002.

  • D. J. Livingstone
    Quantitative structure activity relationships
    in Medicinal Chemistry: Principle and Practice, Second Edition, F. D. King (Ed.), Royal Society of Chemistry, 215-242, 2002.
    ISBN: 978-0-85404-631-7

  • D. J. Livingstone, R. Greenwood, R. Rees and M. D. Smith
    Modelling mutagenicity using properties calculated by computational chemistry
    SAR QSAR Environ. Res., 13, 21-33, 2002.

  • D. T. Manallack, W. R . Pitt, E. Gancia, J. G. Montana, D. J. Livingstone, M. G. Ford and D. C. Whitley
    Selecting screening candidates for kinase and G protein-coupled receptor targets using neural networks
    Journal of Chemical Information and Computer Sciences, 42, 1256-1262, 2002.

  • J. R. Smith, P. A. Cox, N. M. Ratcliffe and S. A. Campbell
    Conducting polymers as coatings: electrochemical and density functional theory investigations of the polymerisation of (Z)-a,b-2-diarylacrylonitriles.
    Transactions of the Institute of Metal Finishing, 80, 52-55, 2002.

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  • F. J. Carver, C. A. Hunter, P. S. Jones, D. J. Livingstone, J. F. McCabe, E. M. Seward, P. Tiger and S. E. Spey
    Quantitative measurements of edge-to-face aromatic interactions by using chemical double-mutant cycles
    Chemistry, 7(22), 4854-62, 2001.

  • A.B.M.N.U. Chowdhury, G. B. Bremer, D. W. Salt, P. Miller and M. G. Ford
    A novel method of delivering Blumeria graminis f. sp. hordei spores for laboratory experiments.
    Crop Protection, 22, 917-922, 2001.

  • A.B.M.N.U. Chowdhury, P. Jepson, P. E. Howse and M. G. Ford
    Leaf surfaces and the bioavailability of pesticide residues.
    Pestic. Manag. Sci., 57, 403-412, 2001.

  • A. S. Dimoglo, N. M. Shivets, I. V. Tetko and D. J. Livingstone
    Electronic-topological investigation of the structure-acetylcholinesterase inhibitor activity relationship in the series of N-benzylpiperidine derivatives
    Quant. Struct.-Act. Relat., 13, 31-45, 2001.

  • M. J. Maple, E. F. Philp, A. M. Z. Slawin, P. Lightfoot, P. A. Cox and P. A. Wright
    Azamacrocycles and the azaoxacryptand 4,7,13,16,21,24-hexaoxa-1,10-diazabicyclo[8.8.8]hexacosane as structure-directing agents in the synthesis of microporous metalloaluminophosphates.
    Journal of Materials Chemistry, 11, 98-104, 2001.

  • R. Garcia, E. F. Philp, A. M. Z. Slawin, P. A. Wright and P. A. Cox
    Nickel complexed within an azamacrocycle as a structure directing agent in the crystallization of the framework metalloaluminophosphates STA-6 and STA-7.
    Journal of Materials Chemistry, 11, 1421-1427, 2001.

  • V. V. Kovalishyn, I. V. Tetko, A. I. Luik, J. R. Chretien and D. J. Livingstone
    Application of neural networks using the volume learning algorithm for quantitative study of the three-dimensional structure-activity relationships of chemical compounds
    Russ. J. Bioorg. Chem., 27, 267-77, 2001.

  • D. J. Livingstone, M. G. Ford, J. J. Huuskonen and D. W. Salt
    Simultaneous prediction of aqueous solubility and octanol/water partition coefficients based on descriptors derived from molecular structure
    J. Comp.-Aided Mol. Des., 15 (8), 741-752, 2001.

  • I. V. Tetko, V. V. kovalishyn and D. J. Livingstone
    Volume learning algorithm artificial neural networks for 3d QSAR studies
    J. Med. Chem., 44, 2411-20, 2001.

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  • A.P. Bisson, F.J. Carver, D.S. Eggleston, R.C. Haltiwanger, C.A. Hunter, D.J. Livingstone, J.F. McCabe, C. Rotger and A.E. Rowan
    Synthesis and Recognition Properties of Aromatic Amide Oligomers: Molecular Zippers
    J. Am. Chem. Soc., 122, 8856-68, 2000.

  • F. R. Burden, M. G. Ford, D. C. Whitley and D. A. Winkler
    The use of automatic relevance determination in QSAR studies using Bayesian Neural Networks
    J. Chem. Inf. Comput. Sci., 40, 1423-1430, 2000.

  • J. J. Huuskonen, D. J. Livingstone and I. V. Tetko
    Neural Network Modeling for Estimation of Partition Coefficient Based on Atom-Type Electrotopological State Indices
    J. Chem. Inf. Comput. Sci., 40, 947-955, 2000.

  • J.J. Huuskonen, J. Rantanen and D.J. Livingstone
    Prediction of Aqueous Solubility for a Diverse Set of Organic Compounds Based on Atom-type Electrotopological State Indices
    Eur. J. Med. Chem., 35, 1081-8, 2000.

  • V.E. Kuz'min, A.G. Artemenko, N.A. Kovdienko, I.V. Tetko, D.J. Livingstone
    Lattice Model for QSAR Studies
    J. Mol. Model, 6, 517-26, 2000.

  • D. J. Livingstone
    The Characterization of Chemical Structures Using Molecular Properties. A Survey
    Journal of Chemical Information and Computer Sciences, 40, 195-209, 2000.

  • I.V. Tetko, T.I. Aksenova, V.V. Volkovich, T.N. Kasheva, D.V. Filipov, A.E.P. Villa, W.J. Welsh and D.J. Livingstone
    Polynomial Neural Network for Linear and Non-linear Model Selection
    In Quantitative-Structure Activity Relationship Studies on WWW
    SAR QSAR Environ. Res., 11, 263-80, 2000.

  • D. C. Whitley and M. G. Ford
    Topological Motifs for Drug Design
    Computation in Cells: Proceedings of an EPSRC Emerging Computing Paradigms Workshop
    University of Hertfordshire, Department of Computer Science, Technical Report No: 345, pp. 83-87, April 2000.

  • D. C. Whitley, M. G. Ford and D. J. Livingstone
    Unsupervised Forward Selection: A Method for Eliminating Redundant Variables
    J. Chem. Inf. Comput. Sci., 40, 1160-1168, 2000.
    doi: 10.1021/ci000384c

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