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.
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)
Elena VatagaTechnical Staff, iSolutions
Petrina ButlerAdministrative Staff, Research and Innovation Services