My research focusses on the development of new methods and software for biomolecular simulation. I am particularly interested in developing novel Monte Carlo algorithms for sampling multiscale models, 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 systems modelled using multiscale quantum mechanics / molecular mechanics (QM/MM) Hamiltonians, and am applying these ideas 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 am developing a new method that uses the flexibility of Sire to calculate absolute binding free energies using the Gibbs Ensemble. 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.

Publications:


Woods, C. J., Brown, P., Manby, F. R., "Multicore Parallelization of Kohn-Sham Theory", J. Chem. Theo. Comput., 5, 1776-1784, 200, doi:10.1021/ct900138j


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


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


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., 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

Links:


http://siremol.org

(website for Sire)


http://protoms.org

(website for ProtoMS)


http://chryswoods.com/beginning_perl

(my Perl workshop)


http://chryswoods.com/beginning_python

(my python workshop)


http://chryswoods.com/beginning_openmp

(my openmp workshop)


http://www.chm.bris.ac.uk/pt/pctl/cccpracticals

(website for the CCC practicals)