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Modelling of Molecule Flexibility for Interactive Docking (LAYCOCKSU20SCIO)

Project Description

Interactive Molecular Docking tools put the user in charge of the docking process enabling them to guide the ligand towards the docking site. A key application is in Structure-Based Drug Design where the structure of the target receptor has been solved and the binding site is normally known. In the development of a new therapeutic drug molecule, a few lead molecules will have been identified and then interactions with the binding site can be investigated. When incorporating a haptic feedback device the user can feel the forces of interaction between the ligand and receptor. However, the forces must be computed within 2ms and this imposes a computational challenge when considering the flexibility of the molecular structures. Adapted MD software has been developed to allow users to apply forces via haptic feedback devices during MD simulations, the best known example being Interactive MD[1]. Other approaches include Bolopion et al. [2] who developed a tool that allows the user to interact with a molecular simulation based on quasi-statics, and another which minimizes the potential energy of a protein-ligand system [3]. Laycock and Hayward developed software for haptic-assisted molecular docking involving receptor flexibility [4] (see and this PhD opportunity builds on this by developing methods for simulating ligand flexibility.

For more information on the supervisor for this project, please go here:

This is a PhD programme.

The start date of the project is 1 October 2020.

The mode of study is full-time. The studentship length is 3 years.

Entry requirements:

Acceptable first degree in Computing Science or related degree.

The standard minimum entry requirement is 2:1.

Funding Notes

This PhD project is in a competition for a Faculty of Science funded studentship. Funding is available to UK/EU applicants and comprises home/EU tuition fees and an annual stipend of £15,009 for 3 years. Overseas applicants may apply but they are required to fund the difference between home/EU and overseas tuition fees (which for 2019-20 are detailed on the University’s fees pages at View Website . Please note tuition fees are subject to an annual increase).


[1] Stone, J., et al., A System for Interactive Molecular Dynamics Simulation, in ACM SIGGRAPH, 2001. p. 191–194.

[2] Bolopion, A., et al., Comparing position and force control for interactive molecular simulators with haptic feedback. Journal of Molecular Graphics & Modelling, 2010. 29(2): p. 280-289.

[3] Daunay, B. and S. Regnier, Stable six degrees of freedom haptic feedback for flexible ligand-protein docking. Computer-Aided Design, 2009. 41(12): p. 886-895.

[4] Matthews, N., et al., Haptic-Assisted Interactive Molecular Docking Incorporating Receptor Flexibility. Journal of Chemical Information and Modeling, 2019. 59(6): p. 2900-2912.

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