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.


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


(website for Sire)

(website for ProtoMS)

(my Perl workshop)

(my python workshop)

(my openmp workshop)

(website for the CCC practicals)