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Department of Chemistry

 

I develop enhanced sampling methods for complex chemical systems. Classical examples of complex chemical systems are polymers and proteins,  clusters, metastable crystalline solids,molecules on surfaces, structural glasses and spin glasses, and more abstract systems one encounters in the form of combinatorial optimization problems such as the travelling salesman problem or the graph bipartitioning problem.

Of particular interest is the difference in folding behaviour of designed and natural proteins of similar shapes and sizes. To fold on biologically relevant time scales, proteins have evolved funnelled energy landscapes with minimal energetic trapping. Designed proteins, that have not had the benefit of evolution often suffer from misfolding and kinetic trapping. I look at the differences between designed and naturally evolved proteins through the lens of their potential energy surface.

Current work focusses on elucidating folding pathways in knotted proteins.

Recent publications:

  1. Go-Kit: A Tool To Enable Energy Landscape Exploration of Proteins
    J. Chem. Inf. Model (2019). (DOI: 10.1021/acs.jcim.9b00007)
  2. Energy landscape of the designed protein Top7
    J. Phys. Chem. B, 2018, 122 (51), pp 12282–12291 (DOI: 10.1021/acs.jpcb.8b08499)
  3. Applications of crystal structure prediction–organic molecular structures: general discussion
    Faraday Discuss., 2018, 211, 493-539
  4. The threshold algorithm: Description of the methodology and new developments
    J. Chem. Phys. 147, 152713 (2017) (Editors' Choice)
  5. A Threshold-Minimization Scheme for Exploring the Energy Landscape of Biomolecules: Application to a Cyclic Peptide and a Disaccharide
    J. Chem. Theor. Comput.,J12 (5), 2471-2479,(2017)

 

 

Research Group

Telephone number

01223 763874 (shared)

Email address

sn513@cam.ac.uk