Centre for Molecular Design (CMD)

Research

Current projects

  • Long-term Molecular Dynamics Simulations of Bioactive Peptides
    To elucidate the principles of bioactivity by means of ligand-receptor interactions, it is important to understand the dynamical nature of ligands and receptors even in the unbound state. As a contribution to this understanding, we are studying the molecular dynamics of small peptide-hormones (e.g. Oxytocin and Vasopressin) via Amber forcefield simulations with explicit water solvation, over timescales of several microseconds. The conformational space is analysed, inter alia, with DASH. Possible reaction paths and free energy barriers for conformation-interconversion are calculated using umbrella sampling. This project is carried out in cooperation with the Peptide Research Network of Excellence (PeReNE) as part of the INTERREG IV A France (Channel) England Programme.

Previous projects

  • Selection Bias in Multiple Regression¬†
    When multiple linear regression models are constructed from a large pool of potential independent variables they suffer from an effect known as selection bias, which has the effect of making the resulting models appear more significant than they really are. This phenomenon is being investigated both analytically and using Monte Carlo simulations.
  • Parasurf Project¬†
    A novel QM, non atom based methodology for virtual screening based on molecular surface properties.
  • Zeolite Modelling
    Molecular modelling methods are being applied to inorganic materials to predict and rationalise structures and reaction mechanisms.
  • Mode of Action of Destruxin
    Studies of the mode of action of destruxin, a cyclic hexadepsipeptide, in collaboration with the BBSRC IACR Rothamsted.
  • Non-Structural Database Searching
    The aim of this work is to create an environment in which compounds can be ranked by similarity to a target using not only the structural data, but also other data associated with the compounds (e.g. boiling point, toxicity, etc.).
  • Drug-DNA Interactions
    Molecular mechanics and dynamics methods can be used to rationalise and predict the interactions between drugs and DNA.