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Publications and Presentations

Publications

The following publications report results which were generated using Sire;

  • Shaw, Woods, and Mulholland, "Compatibility of Quantum Chemical Methods and Empirical (MM) Water Models in Quantum Mechanics / Molecular Mechanics Liquid Water Simulations", J. Phys. Chem. Lett., Accepted for publication, 2009.

    doi:10.1021/jz900096p

  • Woods, Manby and Mullholland, "An efficient method for the calculation of quantum mechanics/molecular mechanics free energies", Journal of Chemical Physics, 128, 014109, 2008.

    http://link.aip.org/link/?JCP/128/0141098

    JPC kindly allow authors to provide copies of their papers on their non-commercial websites. If you have access to JCP then please use the above link to obtain the paper, but if you don't, then you can download the paper from here. Please note the following copyright notice.

    Copyright 2008 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics.

Presentations

The following talks have been presented that discuss results generated using Sire, or discuss the design of Sire.

  • "Secret Diary of a Modeller: Confessions from Beyond the Cutting Edge", Christopher Woods

    This talk was presented at the 2008 CEADD conference in London, October 2008. The talk presented the changes in technology and software over the last ten years, and how this is aiding the development of protein-ligand binding free energy methods. Download the slides from here.

  • "Sire: A powerful and flexible framework for molecular simulation", Christopher Woods

    This talk was presented during an industrial visit in March 2008, and described the design of Sire at that date (the design has evolved a little since then, though the talk is still mostly accurate). Download the slides from here.

  • "QM/MM Free Energy Calculations for Rational Drug Design", Christopher Woods

    This talk was presented at the 2008 CCPB annual meeting in Bristol, January 2008. The talk presented the theory behind a novel QM/MM relative free energy method that was implemented in Sire. Download the slides from here.