Publications
- 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
- 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
- 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
- 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
- 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
- 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
- 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.
- 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
- 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.
- 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
- 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
- Shaw, KE, Woods, CJ & Mulholland, AJ, 2010 “QM and QM/MM Approaches to Evaluating Binding Affinities”. Burger’s Medicinal Chemistry, Drug Discovery and Development,
- 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
- Woods, CJ, Brown, P & Manby, FR 2009, “Multicore Parallelization of Kohn-Sham Theory”. Journal of Chemical Theory and Computation, vol 5., pp. 1776-1784
- 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
- 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
- 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
- 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
- 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
- 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,
- 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
- 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
- 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
- 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
- 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
- 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