BBSRC CASE PhD studentship: “Novel computational methods for drug discovery”
- Apply by
- 31st May 2011
- Categories
- AMBER, Bioinformatics, Biomathematics, Biomedical, Biomolecular simulations, C, CASTEP, Complex Systems, Computer Science, Density functional Theory, Fortran, Gaussian, GPU, Gromacs, HECToR, HPC, Iridis, Meshless methods, Molecular Dynamics, Molecular Mechanics, Monte Carlo, Multi-physics, Multi-scale, Multipole methods, NWCHEM, Onetep, Optimisation, Quantum Chemistry, Scientific Computing, Structural biology, Structural dynamics, Systems biology
- Submitter:
- Chris-Kriton Skylaris
This PhD studentship will involve developing and evaluating novel approaches for the more accurate and realistic simulation of biomolecular association, and applying these to predict the interaction of putative drugs with biomolecular systems. A combination of simulation techniques will be used, including classical molecular dynamics, structure optimisation, statistical mechanics approaches for calculating free energies, and ab initio quantum mechanical calculations with Density Functional Theory (DFT). Most importantly, the DFT calculations will be performed at unprecedented large scales, on entire protein assemblies consisting of thousands of atoms by using the ONETEP linear-scaling DFT program. The use of full quantum mechanical models is essential for quantitative (and sometimes even qualitative) understanding of electronic polarization which is ubiquitous and controls drug binding affinity. This project will not only give access to new methods for assessing the likely affinity of proposed drugs with the biological target of interest, but will also aim to address aspects of drug optimisation and will be directed at rationalizing the fundamental mechanisms and modes of action in biomolecular association. The wider implications of this research will be in reducing our dependence on laboratory experimentation for stages of the drug development process.
This is a prestigious BBSRC CASE PhD studentship which is supported by Boehringer Ingelheim who will enhance its tax-free stipend (approximately £16,000 p.a. and subject to annual increase) and will provide periods of placement within the company’s research laboratories in Germany. Academic supervision will be provided by Dr Chris-Kriton Skylaris and further details regarding research themes and projects within the group can be found at http://www.soton.ac.uk/chemistry/about/staff/cks.page .The successful applicant will join a well-established Research Group in the area of computational chemistry with a keen focus on the development of methods for large-scale quantum mechanical calculations and their applications to biomolecular problems and will have access to state-of-the-art supercomputing facilities and the latest developments in the ONETEP package (www.onetep.org). He/She will also be a member of the Computational Systems Chemistry section and will support the ongoing theme of multiscale biomolecular simulation.
Applicants should have a good (preferably first or 2:1) degree in Chemistry, Physics or related subject and a keen interest in computational chemistry and biochemistry. For further details please contact Dr Chris-Kriton Skylaris (c.skylaris@soton.ac.uk). The studentship is open to UK students and also to EU students who fulfil the eligibility criteria set by BBSRC: http://www.bbsrc.ac.uk/web/FILES/Guidelines/studentship_eligibility.pdf