HOME- Bryn Mawr Conference
- Workshops & Training
- 2010 Oxford (Discovery)
- 2010 Oxford (ADMET)
- 2009 Oxford (Discovery)
- Blanchard, H
- Bryant, S
- Coveney, P
- Hardy, B
- Hawkins, P
- Klamt, A
- Knapp, S
- Kranz, M
- Liebeshuetz, J
- Oledzki, P
- Pirok, G
- Wolber, G
- Zamora, I
- Bursary Award
- 2009 Oxford (ADMET)
- 2008 Oxford
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David Wright comes from a physics background having completed a degree in Computational Physics at the University of York in 2003. He moved into biological science in 2006 when he joined the CoMPLEX doctoral training centre at UCL obtaining an MRes and progressing into the PhD program. He is currently completing his PhD investigating the calculation of binding free energies of HIV-1 inhibitors from molecular dynamics simulations at the Centre for Computational Science, whose Director is Prof. Peter V. Coveney. During his time in the group he has also been an active member of the EU project Virolab (http://www.virolab.org) which seeks to enhance existing clinical support tools in the field of HIV treatment.
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Binding Free Energy Calculations
David Wright (University College London)
A common requirement in biological science is to evaluate the binding free energy of drugs with their target enzymes and potentially mutant forms of these proteins. A widely used method to study drug-enzyme interactions in silico is molecular dynamics (MD). One popular way to compute binding free energies from MD simulations is the Molecular Mechanics Poisson Boltzmann Solvent Accessible Surface Area (MMPBSA) methodology. In this session the students will run a short simulation of the HIV-1 protease bound to an inhibitor and use MMPBSA to calculate the binding affinity and discuss the analysis of the results.
This session will also focus on the use of Grid computing in order to obtain the computational power required to achieve converged results from MD simulations. Workshop participants will be introduced to the Binding Affinity Calculator (BAC) system for automated construction, deployment, implementation and post-processing stages of the MD simulations. The aim here is to demonstrate the power of the underlying Application Hosting Environment (AHE) to execute the various stages of the workflow involved in the MMPBSA calculation, in general, across multiple HPC and grid-based resources. In addition the use of such a system to evaluate the effects of drug resistance mutations on HIV-1 protease mutations from within the Virolab Virtual Laboratory will be presented.
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