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Postgraduate research project

Enhancing protein and ligand sampling in molecular simulations by fully adaptive simulated tempering (FAST)

Fully funded (UK only)
Type of degree
Doctor of Philosophy
Entry requirements
2:1 honours degree (View full entry requirements)
Faculty graduate school
Faculty of Engineering and Physical Sciences
Closing date

About the project

Binding free energy calculations are a widely used technique in the pharmaceutical industry to identify molecules which may be usefully developed into drug candidates. However, these methods are not always successful, and it is not obvious a priori which systems will perform well, and on which systems the methods will struggle.

In cases where inaccurate free energies are generated, the errors may be ascribed to either inadequate sampling, or a force field which does not adequately represent the molecular interactions in the system. In this project you will address the sampling problem.

Through a collaboration with AstraZeneca and GSK, we have developed a new procedure, Fully Adaptive Simulated Tempering (FAST), to address the sampling problem. While preliminary data suggest that the approach has significant promise, further validation and optimisation are required for its true potential to be known.

In this project you will work in close collaboration with scientists at AstraZeneca and GSK to explore the domain of applicability of FAST, and optimise its performance.

You will spend at least 3 months of this 3 ½ year studentship working at AstraZenenca, where you will learn how computer modelling is applied to drug discovery.

At the University of Southampton you will be supervised by Professor Jonathan Essex, an expert in the development and application of computer simulation methodology to biological systems.

You will also be supervised by Dr Michael Bodnarchuk (AstraZeneca) and Dr Ian Wall (GSK), both of whom are leading industrial computational chemists.



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