About

I am Christopher Woods, a postdoctoral researcher at the Centre for Computational Chemistry, University of Bristol, currently funded by the EPSRC.

I have developed two major pieces of molecular simulation software; Sire, and ProtoMS. I use these programs to develop new methods to enhance the accuracy and precision of biomolecular simulations. I am currently developing new methods that allow for rapid Monte Carlo sampling of biomolecular systems modelled using multiscale quantum mechanics / molecular mechanics (QM/MM) and coarse grain (CG) / MM / QM Hamiltonians, and am applying this methodology to the calculation of relative protein/ligand binding free energies, and to investigate the free energy profiles of enzyme-catalysed reactions. I am also working on improved methods of sampling protein conformational change during free energy simulations, and have developed a new method, called the water-swap reaction coordinate (WSRC), that uses the power of Sire to calculate absolute protein-ligand binding free energies. Prior to this, I developed the RETI free energy method, which uses replica exchange moves to enhance sampling and reduce random error in relative free energy calculations.

I have over ten years experience writing scientific software, and am an experienced Fortran, C++, Perl and Python programmer, and write parallel performance software using SSE, OpenMP, MPI. I have also developed code for numerical accelerators (e.g. co-developing the ClearSpeed accelerated density functional theory - DFT - implementation in the Molpro quantum chemistry program and working with OpenCL and CUDA).

Selected Publications

• Woods, C. J., Malaisree, M., Pattarapongdilok, N., Sompornpisut, P., Hannongbua, S., Mulholland, A. J., "Long time scale GPU dynamics reveal the mechanism of drug resistance of the dual mutant I223R/H275Y neuraminidase from H1N1-2009 influenza virus.", Biochemistry, 29, 4364-4375, 2012 DOI:10.1021/bi300561n
• Woods, C. J., Malaisree, M., Hannongbua, S., Mulholland, A.J., “A water-swap reaction coordinate for the calculation of absolute protein-ligand binding free energies”, J. Chem. Phys. 134, 054114, 2011 DOI:10.1063/1.3519057
• Shaw, K. E., Woods, C. J., Mulholland, A. J., "QM and QM/MM Approaches to Evaluating Binding Affinities", Burger's Medicinal Chemistry, Drug Discovery and Development, Published Online: 15 SEP 2010
  DOI: 10.1002/0471266949.bmc143
• Brown, P, Woods, C.J., McIntosh-Smith, S., Manby, F.R.,
  "A massively multicore parallelization of the Kohn-Sham energy gradients", J. Comp. Chem., 31, 2008-2013, 2010
  doi:10.1002/jcc.21485
• Shaw, K. E., Woods, C. J., Mulholland, A. J., "Compatibility of Quantum Chemical Methods and Empirical (MM) Water Models in Quantum Mechanics / Molecular Mechanics Liquid Water Simulations", J. Phys. Chem. Lett., 1, 219-223, 2010
  doi:10.1021/jz900096p
• Woods, C. J., Brown, P., Manby, F. R., "Multicore Parallelization of Kohn-Sham Theory", J. Chem. Theo. Comput., 5, 1776-1784, 2009
  doi:10.1021/ct900138j
• Pentikäinen, U., Shaw, K. E., Senthilkumar, K., Woods, C.J., Mulholland, A.J.,
  "Lennard-Jones Parameters for B3LYP-CHARMM27 QM/MM modelling of Nucleic Acid Bases",
  J. Chem. Theo. Comput., 5, 396-410, 2009
  doi:10.1021/ct800135k
• Brown, P, Woods, C.J., McIntosh-Smith, S., Manby, F.R.,
  “Massively Multicore Parallelization of Kohn-Sham Theory”,
  J. Chem. Theo. Comput., 4, 1620-1626, 2008
  doi:10.1021/ct800261j
• Woods, C.J., Mulholland, A.J.,
  “Multiscale modelling of biological systems”,
  in Royal Society of Chemistry Special Periodicals Review: Chemical Modelling: Application and Theory, Ed. Hinchliffe A., 5, 13-50, 2008
  link
• van der Kamp, M.W., Shaw, K.E., Woods, C.J., Mulholland, A.J.,
  “Biomolecular simulation and modelling: status, progress and prospects”,
  J. R. Soc. Interface, 2008
  doi:10.1098/rsif.2008.0105.focus
• Lodola, A., Woods, C.J., Mulholland, A.J.,
  “Applications and Advances of QM/MM Methods in Computational Enzymology”,
  Ann. Reports. Comput. Chem., 4, 155-169, 2008
  link
• Woods, C.J., Manby F.R., Mulholland A.J.,
  “An efficient method for the calculation of quantum mechanics/molecular mechanics free energies”,
  J. Phys. Chem., 128, 014109, 2008
  doi:10.1063/1.2805379
• Woods. C.J. et al.,
  “Grid computing and biomolecular simulation”,
  Phil. Trans. Roy. Soc. A, 363,
  2017-2035, 2005
  doi:10.1098/rsta.2005.1626
• Woods, C.J., King, M.A., Essex, J.W.,
  “Replica-exchange-based free-energy methods”,
  in New Algorithms for Molecular Simulation, Eds. Leimkuhler B. et al.,
  ISBN: 3-54025542-7, 251-257, 2005
  link
• Woods, C.J., King, M.A., Essex, J.W.,
  “Enhanced configurational sampling in binding free energy calculations”,
  J. Phys. Chem. B, 107, 13711-13718, 2003
  doi:10.1021/jp036162
• Woods, C.J., King, M.A., Essex, J.W.,
  “The development of replica-exchange-based free-energy methods”,
  J. Phys. Chem. B, 107, 13703-13710, 2003
  doi:10.1021/jp0356620
• Woods, C.J., et al.,
  “Fluoride-selective binding in a new deep cavity calix[4]pyrrole: Experiment and theory”,
  J. Am. Chem. Soc., 124, 8644-8652, 2002
  doi:10.1021/ja025572t
• Woods, C.J., King, M.A., Essex, J.W.,
  “The configurational dependence of binding free energies: A Poisson-Boltzmann study of Neuraminidase”,
  J. Comput. Aid. Mol. Des., 15, 129-144, 2001
  doi:10.1023/A:1008197913568