Haptic Interaction for Molecular Docking (LAYCOCKU16SF)
Proteins are molecular machines involved in every biological process. A fair amount is known concerning their structures, although relatively little is known about their flexibility. The understanding of the processes involved in the binding of small molecules (ligands) to proteins is crucial for our understanding of protein mechanism. We can attempt to understand the forces involved by placing the ligand at various positions from a protein’s binding site, in a process known as “docking”. Docking is often combined with molecular graphics software so one can see the relative locations and orientations of the protein and ligand. This can be enhanced by the use of a haptic device where the user can also feel the forces of interaction . This has great advantages as it couples our sense of sight with our sense of touch (haptic system) and creates an intuitive approach that has often been a path to discovery at the human level.
This PhD project will involve the development of advanced haptics software for molecular docking. This software will be aimed at those that work in the pharmaceutical industries in computer-aided structure-based drug design. This work will build on our previous research in this area which has resulted in two software tools. The first enables the user to explore rigid molecules by interacting with the solvent accessible surface . The second enables the user to apply forces to a flexible model of a protein . For more information please visit http://www.haptimol.com
This project is offered on a self-funding basis. It is open to applicants with funding or those applying to funding sources. Details of tuition fees can be found at http://www.uea.ac.uk/pgresearch/pgrfees.
A bench fee is also payable on top of the tuition fee to cover specialist equipment or laboratory costs required for the research. The amount charged annually will vary considerably depending on the nature of the project and applicants should contact the primary supervisor for further information about the fee associated with the project.
 F.P. Brooks, M. Ouh-Young Jr, J.J. Battert and P.J. Kilpatrick. Project grope-haptic displays for scientific visualisation. In Proc. of ACM Siggraph, pages 177-185, 1990
 Stocks, M.B., Hayward, S. and Laycock, S.D., Interacting with the biomolecular solvent accessible surface via a haptic feedback device, BMC Structural Biology, 9:69, 2009.
 Stocks, Matthew, Laycock, Stephen and Hayward, Steven (2011) Applying forces to elastic network models of large biomolecules using a haptic feedback device. Journal of Computer-Aided Molecular Design, 25 (3). pp. 203-211.