Publications

  1. Loeffler, H, Michel, J & Woods, CJ, 2015, “FESetup: Automating Setup for Alchemical Free Energy Simulations”. Journal of Chemical Information and Modeling, Just Accepted, DOI: 10.1021/acs.jcim.5b00368
  2. Sampson, C, Fox, T, Tautermann, CS, Woods, CJ & Skylaris C-K, 2015 “A ‘Stepping Stone’ Approach for Obtaining Quantum Free Energies of Hydration”. Journal of Physical Chemistry B, vol. 119, pp. 7030-7040
  3. Woods, CJ, Shaw, KE & Mulholland, AJ, 2015, “Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Simulations for Protein–Ligand Complexes: Free Energies of Binding of Water Molecules in Influenza Neuraminidase”. Journal of Physical Chemistry B, vol. 119, pp. 997-1001
  4. Smith, D, Woods, C, Seddon, A & Hoerber, H 2014, “Photophoretic separation of single-walled carbon nanotubes: A novel approach to selective chiral sorting”. Physical Chemistry Chemical Physics, vol 16., pp. 5221-5228
  5. Woods, CJ, Malaisree, M, Michel, J, Long, B, McIntosh-Smith, S & Mulholland, AJ 2014, “Rapid decomposition and visualisation of protein-ligand binding free energies by residue and by water”. Faraday Discussions, vol 169., pp. 477-499
  6. Woods, CJ, Malaisree, M, Long, BJO, McIntosh-Smith, SN & Mulholland, AJ 2013, “Analysis and assay of oseltamivir-resistant mutants of influenza neuraminidase via direct observation of drug unbinding and rebinding in simulation”. Biochemistry, vol 52., pp. 8150-8164
  7. Woods, CJ, Malaisree, M, Long, BJO, McIntosh-Smith, S & Mulholland, AJ 2013, “Computational Assay of H7N9 Influenza Neuraminidase Reveals R292K Mutation Reduces Drug Binding Affinity”. Scientific Reports, vol 3.
  8. Woods, CJ, Malaisree, M, Pattarapongdilok, N, Sompornpisut, P, Hannongbua, S & Mulholland, AJ 2012, “Long Time Scale GPU Dynamics Reveal the Mechanism of Drug Resistance of the Dual Mutant I223R/H275Y Neuraminidase from H1N1-2009 Influenza Virus”. Biochemistry, vol 51., pp. 4364-4375
  9. Woods, CJ, Malaisree, M, Hannongbua, S & Mulholland, AJ 2011, “A water-swap reaction coordinate for the calculation of absolute protein-ligand binding free energies”. Journal of Chemical Physics, vol 134.
  10. Shaw, KE, Woods, CJ & Mulholland, AJ 2010, “Compatibility of Quantum Chemical Methods and Empirical (MM) Water Models in Quantum Mechanics/Molecular Mechanics Liquid Water Simulations”. Journal of Physical Chemistry Letters, vol 1., pp. 219-223
  11. Brown, P, Woods, C, McIntosh-Smith, S & Manby, F 2010, “A massively multicore parallelization of the Kohn-Sham energy gradients”. Journal of Computational Chemistry, vol 31., pp. 2008 - 2013
  12. Shaw, KE, Woods, CJ & Mulholland, AJ, 2010 “QM and QM/MM Approaches to Evaluating Binding Affinities”. Burger’s Medicinal Chemistry, Drug Discovery and Development,
  13. Shaw, KE, Woods, CJ, Mulholland, AJ, 2010, “Compatibility of Quantum Chemical Methods and Empirical (MM) Water Models in Quantum Mechanics / Molecular Mechanics Liquid Water Simulations”. Journal of Physical Chemistry Letters, vol 1, pp. 219-223
  14. Woods, CJ, Brown, P & Manby, FR 2009, “Multicore Parallelization of Kohn-Sham Theory”. Journal of Chemical Theory and Computation, vol 5., pp. 1776-1784
  15. Pentikäinen, U, Shaw, KE, Senthilkumar, K, Woods, CJ & Mulholland, AJ, 2009, “Lennard-Jones Parameters for B3LYP-CHARMM27 QM/MM modelling of Nucleic Acid Bases”. Journal of Chemical Theory and Computation, vol. 5, pp. 396-410
  16. Brown, P, Woods, CJ, McIntosh-Smith, S & Manby, FR, 2008, “Massively Multicore Parallelization of Kohn-Sham Theory”. Journal of Chemical Theory and Computation, vol. 4, pp. 1620-1626
  17. Woods, CJ & Mulholland, AJ, 2008, “Multiscale modelling of biological systems”. in Royal Society of Chemistry Special Periodicals Review: Chemical Modelling: Application and Theory, Ed. Hinchliffe A., vol. 5, pp. 13-50
  18. van der Kamp, MW, Shaw, KE, Woods, CJ & Mulholland, AJ, 2008, “Biomolecular simulation and modelling: status, progress and prospects” Journal of the Royal Society Interface
  19. Lodola, A, Woods, CJ & Mulholland, AJ, 2008, “Applications and Advances of QM/MM Methods in Computational Enzymology”. Annual Reports in Computational Chemistry, vol. 4, pp. 155-169
  20. Woods, CJ, Manby FR & Mulholland AJ, 2008, “An efficient method for the calculation of quantum mechanics/molecular mechanics free energies”. Journal of Chemical Physics, vol. 128,
  21. Woods, CJ, Ng, MG, Johnston, S, Murdock, SE, Wu, B, Tai, K, Fangohr, H, Jeffreys, P, Cox, S, Frey, JG, Sansom, MSP & Essex JW, 2005, “Grid computing and biomolecular simulation”. Philisophical Transactions of the Royal Society A, vol. 363, pp. 2017-2035
  22. Woods, CJ, King, MA & Essex, JW, 2005, “Replica-exchange-based free-energy methods”. in New Algorithms for Molecular Simulation, Eds. Leimkuhler B. et al., ISBN: 3-54025542-7, 251-257
  23. Woods, CJ, King, MA, & Essex, JW, 2003 “Enhanced configurational sampling in binding free energy calculations”. Journal of Physical Chemistry B, vol. 107, pp. 13711-13718
  24. Woods, CJ, King, MA & Essex, JW, 2003, “The development of replica-exchange-based free-energy methods”. Journal of Physical Chemistry B, vol. 107, pp. 13703-13710
  25. Woods, CJ, Camiolo, S, Light, ME, Coles, SJ, Hursthouse, MB, King, MA, Gale, PA & Essex, JW, 2002, “Fluoride-selective binding in a new deep cavity calix[4]pyrrole: Experiment and theory”. Journal of the American Chemical Society, vol. 124, pp. 8644-8652
  26. Woods, CJ, King, MA & Essex, JW, 2001, “The configurational dependence of binding free energies: A Poisson-Boltzmann study of Neuraminidase”. Journal of Computer Aided Molecular Design, vol. 15, pp. 129-144