ProtoMS
ProtoMS is a Monte Carlo simulation package for biomolecular simulations. The code is capable of simulating three different ensembles; NPT, NVT and mVT. In addition, it is capable of performing lambda-dynamics, TI and FEP.
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Projects
Molecular Fragments in Inhibitor Design
Jonathan Essex (Investigator), Michael Bodnarchuk
Fragment-Based Drug Discovery (FBDD) has emerged as an important tool in the drug discovery process. Instead of screening entire drug molecules, FBDD screens molecular fragments; constituents which make up drug molecules. A computational approach to identifying fragment binding is currently being sought which also yield binding free energy estimation.
The application and critical assessment of protein-ligand binding affinities
Jonathan Essex (Investigator), Ioannis Haldoupis
A method that can accurately predict the binding affinity of small molecules to a protein target would be imperative to pharmaceutical development due to the time and resources that could be saved. A head-to-head comparison of such methodology, ranging from approximate methods to more rigorous methods, is performed in order to assess their accuracy and utility across a range of targets.
Water molecules in drug development: can we predict drug affinity when water molecules are involved?
Jonathan Essex (Investigator), Hannah Bruce Macdonald, Christopher Cave-Ayland
Water molecules are often found to be involved in drug-protein binding and can influence the effectiveness of a drug. We aim to aid drug design by calculating the energies involved with complexes of drugs, proteins and water molecules to predict the affinities of drug molecules.
Water Molecules in Protein Binding Sites
Jonathan Essex (Investigator), Michael Bodnarchuk
Water molecules are commonplace in protein binding sites, although the true location of them can often be hard to predict from crystallographic methods. We are developing tools which enable the location and affinity of water molecules to be found.
People
Jonathan EssexProfessor, Chemistry (FNES)
Michael BodnarchukPostgraduate Research Student, Chemistry (FNES)
Hannah Bruce MacdonaldPostgraduate Research Student, Chemistry (FNES)
Christopher Cave-AylandPostgraduate Research Student, Electronics and Computer Science (FPAS)
Ioannis HaldoupisPostgraduate Research Student, Chemistry (FNES)
Elena VatagaTechnical Staff, iSolutions
Petrina ButlerAdministrative Staff, Research and Innovation Services