Publications

  1. Oliveira, A. S. F., Edsall, C. J., Woods, C. J., Bates, P., Nunez, G. V., Wonnacott, S., Bermudez, I., Ciccotti, G., Gallagher, T., Sessions, R. B. & Mulholland, A. J., 2019, A General Mechanism for Signal Propagation in the Nicotinic Acetylcholine Receptor Family, Journal of the American Chemical Society, 141, 19953-19958
  2. Hedges, L. O., Mey, A. S. J. S., Laughton, C., Gervasio, F. L., Mulholland, A. J., Woods, C. J. & Michel, J., 2019, BioSimSpace: An interoperable Python framework for biomolecular simulation, Journal of Open Source Software, 4, 1831
  3. Vragniau, C., Bufton, J. C., Garzoni, F., Stermann, E., Rabi, F., Terrat, C., Guidetti, M., Josserand, V., Williams, M., Woods, C. J., Viedma, G., Bates, P., Verrier, B., Chaperot, L., Schaffitzel, C., Berger, I. & Fender, P., 2019, Synthetic self-assembling ADDomer platform for highly efficient vaccination by genetically encoded multiepitope display, Science Advances, 5, 2375-2548
  4. Abraham, M., Apostalov, R., Barnoud, J., Bauer, P., Blau, C., Bonvin, A., Chavent, M., Chodera, J., Čondić-Jurkić, K., Delemotte, L., Grubmüller, H., Howard, R., Jordan, E. J., Lindahl, E., Ollila, O. H. S., Selent, J., Tiemann, J., Smith, D., Stansfeld, P., Trellet, M., Woods, C. J. & Zhmurov, A., 2019, Sharing Data from Molecular Simulations, Journal of Chemical Information and Modelling, 59, 4093-4099
  5. Raza, S., Ranaghan, K., Van der Kamp, M., Woods, C., Mulholland, A. & Azam, S. S., 2019, Visualizing protein–ligand binding with chemical energy-wise decomposition (CHEWD): application to ligand binding in the kallikrein-8 S1 Site, Journal of Computer-Aided Molecular Design, 33, 461-475
  6. Haldar, S., Comitani, F., Saladino, G., Woods, C., Van der Kamp, M., Mulholland, A. & Gervasio, F. L., 2018, A multiscale simulation approach to modelling drug-protein binding kinetics, Journal of Chemical Theory and Computation
  7. Callegari, D., Ranaghan, K., Woods, C., Minari, R., Tiseo, M., Mor, M., Mulholland, A. & Lodola, A., 2018, L718Q mutant EGFR escapes covalent inhibition by stabilizing a non-reactive conformation of the lung cancer drug osimertinib, Chemical Science
  8. Calabrò, G., Woods, C. J., Powlesland, F., Mey, A. S. J. S., Mulholland, A. J. & Michel, J., 2016, Elucidation of Nonadditive Effects in Protein-Ligand Binding Energies: Thrombin as a Case Study, Journal of Physical Chemistry B, 120, 5340-5350
  9. Loeffler, H, Michel, J & Woods, CJ, 2015, “FESetup: Automating Setup for Alchemical Free Energy Simulations”. Journal of Chemical Information and Modeling
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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.
  16. 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
  17. 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.
  18. 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
  19. 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
  20. Shaw, KE, Woods, CJ & Mulholland, AJ, 2010 “QM and QM/MM Approaches to Evaluating Binding Affinities”. Burger’s Medicinal Chemistry, Drug Discovery and Development,
  21. 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
  22. Woods, CJ, Brown, P & Manby, FR 2009, “Multicore Parallelization of Kohn-Sham Theory”. Journal of Chemical Theory and Computation, vol 5., pp. 1776-1784
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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,
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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