Research

Molecular Modelling • Metalloenzymes • Protein Dynamics • Machine learning

Molecular modelling in combination with mathematical modelling and machine learning allows atomistic insight into the behaviour of molecular biological systems. We use and develop tools to improve protein models that allow us to study small molecule protein interactions, protein protein interactions, as well as protein mutations. One particular research focus are metalloenzymes that give rise to antibiotic resistances in bacteria.

Software

BioSimSpace is the largest of the software projects we were involved in. It is an interoperable simulation frame work that allows easy setup, simulation and analysis of simple molecular dynamics simulations, alchemical free energy simulations or metadynamics simulations.

It is a collaborative software project and further contributions and suggestions for improvements are always welcome and if you find any issues just report the problem on github.

BioSimSpace builds on Sire and SOMD, which uses OpenMM to accelerate molecular dynamics simulations for GPU usage. It allows fast simulations of alchemical free energy calculations, which have recently been put into commercial tools such as Cresset’s Flare.

Sire is a molecular software library in its own right and can do many more powerful things than just run alchemical free energy calculations with SOMD. It is also an open source tools and all code is available on github.

In general all our code can be found on github, so feel free to have a look at what is going on at the moment. All feedback is always welcome.