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Development of a neutron macromolecular crystallography (NMX) refinement software module and its implementation in the Refmac5 package of the CCP4 suite

  • Full or part time
  • Application Deadline
    Applications accepted all year round
  • Funded PhD Project (European/UK Students Only)
    Funded PhD Project (European/UK Students Only)

Project Description

To start
01/01/2019

Award
A 3 year PhD studentship

School
Basic & Medical Biosciences

Supervisors
Professor Roberto Steiner & Dr Garib N Murshudov

Exceptional opportunity for a student with an interest in software development applied to biological problems.

Project summary
Macromolecular X-ray crystallography (MX) does not typically allow the direct visualization of hydrogen atoms. Yet, the precise knowledge of H-bonding networks, water molecule orientations and correct protonation states are often key to the understanding of biological processes, such as enzyme mechanisms, ligand binding preferences, and can help guide structure-based drug design. Neutron macromolecular crystallography (NMX) is a powerful complementary technique to MX for locating H atoms and is used to provide information on the protonation states of amino acid residues, the exact identity of solvent molecules, and the nature of bonds involving H atoms.

The main objective of this project is to extend the current capabilities of the CCP4 refinement package Refmac5 [1], one of the main crystallographic programs and employed by users all around the world, by incorporating a novel software module that will allow the refinement of macromolecular crystallographic structures using neutron diffraction data either with or without support of X-ray diffraction data. The work will be partly carried out at the LMB-MRC in Cambridge and at King’s College London, taking advantage of the exceptional research environment of these world-class institutions.

Garib Murshudov (LMB-MRC, Cambridge) is the main author of the program Refmac5 and an expert in the application of computational methods to structural biology. Roberto Steiner (King’s College London), is a leading structural biologist with experience in software development.

The student should have a strong background in scientific programming and an interest in software development applied to biological problems. A background in Biology is not required and training will be offered to contextualise the software development work. The interested student will also have the opportunity to measure NMX data at the Institut Laue-Langevin in Grenoble (France) on available projects. This is an excellent opportunity for an ambitious student to gain exposure in the field as there will be several opportunities to present research results at CCP4-sponsored workshops and meetings.

Academic requirement
Minimum Upper Second (above 60%) BSc degree in Physics, Computer Science, Mathematics, Chemistry or an MSc in relevant area.

Training
All students are regularly notified about skills development opportunities through a monthly Postgraduate Research Newsletter. Participation in the annual Postgraduate Research Symposium is compulsory for all students and provides an opportunity to improve science communication and presentation skills.

All postgraduate students in the Randall Centre present their research in seminars to the whole division as well as to their research groups. Opportunities are available for postgraduate students to present their work at national and international scientific meetings. Our postgraduate students also assist with teaching of undergraduates as demonstrators in practical classes or leading tutorials.

How to apply
Please apply online at https://apply.kcl.ac.uk/ following these steps:

1. Register a new account /login.

2. Open a new application

3. Under Choose a programme:
a. Select - Research programme
b. Keywords- enter Randall
c. Select from the programmes listed ‘Randall Centre of Cell and Molecular Biophysics MPhil/PhD (Full-time)’ (your application cannot be considered if submitted under the incorrect programme)
d. Start point will come up with 1 October 2018. However, if you would prefer to be considered for the start point 1 January 2019 please indicate in your personal statement.

4. Complete the application – IMPORTANT: Under Supporting statement please give the project title and reference 18/RDCMB/S03 and Professor Roberto Steiner as the identified supervisor. Please upload a personal statement under document category

Interviews will be held on a rolling basis.

Closing date
Open until suitable candidate is found

Contact information for enquiries
It is highly recommended to informally approach Roberto Steiner at before making an application. For administrative and application process enquiries, please contact Helen Rudkin at

Funding Notes

Sponsor
Collaborative Computational Project 4

Stipend
Research Council rate (£16,777 2018/19 tax free)

References

Reference [1] Murshudov GN, Skubák P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-67. doi: 10.1107/S0907444911001314.

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