Interactive docking of flexible molecules in VR (HAYWARDS_U23CMP) at University of East Anglia on FindAPhD.com

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Dr S Hayward, Dr S Laycock No more applications being accepted Competition Funded PhD Project (UK Students Only)

Norwich United Kingdom Bioinformatics Biophysics Computational Chemistry Computer Graphics

About the Project

Interactive Molecular Docking tools put the user in charge of the process of bringing two molecules (e.g., a drug molecule and a protein) to their binding pose. A key application is in structure-based drug design (SBDD) where the atomic structure of the target receptor is known. In the development of a new therapeutic drug molecule, lead molecules will have been identified and interactions of these lead molecules with the target receptor binding site can be investigated. Towards this goal we have developed an interactive docking tool, DockIT [1].

Molecules are generally flexible, and accurate modelling molecular flexibility is critical. One approach is to use the method of linear response. We have implemented this for a single molecule, the other remaining rigid [2,3]. The project aims to develop methods for modelling flexibility in both molecules leading to a tool where mutual relaxation of both molecules occurs upon binding leading to a better understanding of the binding process, and new insights for SBDD.

DockIT is VR enabled and part of the project will also be to incorporate these features within a VR environment so that the process of interactive docking is easy and intuitive. See www.haptimol.co.uk for more information on DockIT and related tools.

Additional information:

For more information on the supervisor for this project, please visit the UEA website www.uea.ac.uk

Entry requirements: Acceptable first degree in Computing Science, Physics, Chemistry, Engineering.

Start date: October 2023

Funding Notes

This PhD project is in a competition for studentships allocated to the School of Computing Sciences as a direct result is increased PGT student fee income for the MSc Courses in Cyber Security, Data Science and Computing Sciences. All successful candidates will be expected to support PGT Lab sessions from October 2023 and related activities as allocated in support of these programmes within the working hours permitted for full-time Postgraduate Researchers.
Funding comprises ‘home’ tuition fees and an annual stipend (2022/23 rate is £17,668, 2023/24 tbc) for a maximum of 3 years.

Where will I study?

University of East Anglia

We’re one of the UK’s leading research institutions, ranked 10th in the UK for the quality of our research outputs and with more than 1,500 research students.