– a brief bio
Under the supervision of simulation masterminds, Mark Sansom (Oxford University) and Robert Best (NIH), I'm working on membrane protein folding.
I used to work as a scientific associate in D. E. Shaw Research, New York City. The focus of this work (among other things) were transient/cryptic protein pockets identified via ANTON simulations in phosphatases PTP1B and Ship2. The aim was to predict small molecules that would bind to these pockets.
I did my undergraduate work in Oxford, studying Biochemistry, earning an MBioch with honors
and a medal from the Queen and Mick Jagger.
My graduate project was in Groningen, Netherlands working on molecular dynamics simulations.
- Ligandbook - an online repository for small and drug-like molecule force field parameters (submitted)
- Convergence and Sampling in Determining Free Energy Landscapes for Membrane Protein Association DOI: 10.1021/acs.jpcb.6b08445
- Lipid Loving ANTs: Cardiolipin Interactions and the Organization of the Adenine Nucleotide Translocase in Model Mitochondrial Membranes DOI 10.1021/acs.biochem.6b00751
- J. Domański, S.J. Marrink, L.V. Schäfer, Transmembrane
helices can induce domain formation in crowded model membranes,
Biochim. Biophys. Acta (2012) 984-94 21884678
- J. Domański, P.J. Stansfeld, M.S. Sansom, O. Beckstein, Lipidbook:
a public repository for force-field parameters used in membrane
simulations, J. Membr. Biol. (2010) 255-8 20700585
A public repository for OPLS-AA ligand parameters.
Older brother to ligandbook.
A top-notch MD data analysis library.
A "Sargasso Sea" of assorted notes, unfinished projects.