Introduction
– 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.

Publications

  • 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

Other work

Ligandbook

A public repository for OPLS-AA ligand parameters.

Lipidbook

Older brother to ligandbook.

MDAnalysis

A top-notch MD data analysis library.

Technical blog

A "Sargasso Sea" of assorted notes, unfinished projects.