Starting from 2017, I have been a co-founder and CTO at Labstep. Labstep set out to make scientists more productive and creative. So far this involved building a software tool at www.labstep.com.
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.
E Yamamoto, J Domański, FB Naughton, RB Best, AC Kalli, PJ Stansfeld, MSP Sansom,
Multiple Lipid Binding Sites Determine the Affinity of PH Domains for Phosphoinositide-Containing Membranes
Richard J Gowers, Max Linke, Jonathan Barnoud, Tyler John Edward Reddy, Manuel N Melo, Sean L Seyler, Jan Domanski, David L Dotson, Sébastien Buchoux, Ian M Kenney, Oliver Beckstein,
MDAnalysis: a Python package for the rapid analysis of molecular dynamics simulations
Matthieu Chavent, Dimple Karia, Antreas C Kalli, Jan Domański, Anna L Duncan, George Hedger, Phillip J Stansfeld, Elena Seiradake, E Yvonne Jones, Mark SP Sansom,
Interactions of the EphA2 kinase domain with PIPs in membranes: implications for receptor function
J. Domański, M.S.P. Sansom, P.J. Stansfeld, R.B. Best,
Balancing Force Field Protein–Lipid Interactions To Capture Transmembrane Helix–Helix Association
J. Domański, O. Beckstein, B. Iorga,
Ligandbook - an online repository for small and drug-like molecule force field parameters
J. Domański, G. Hedger, R. Best, P.J. Stansfeld, M.S.P. Sansom,
Convergence and Sampling in Determining Free Energy Landscapes for Membrane Protein Association
G. Hedger, S.L. Rouse, J. Domański, M. Chavent, H. Koldsø, M.S.P. Sansom,
Lipid Loving ANTs: Cardiolipin Interactions and the Organization of the Adenine Nucleotide Translocase in Model Mitochondrial Membranes
J. Domański, S.J. Marrink, L.V. Schäfer,
Transmembrane helices can induce domain formation in crowded model membranes,
Biochim. Biophys. Acta (2012) 984-94
J. Domański, P.J. Stansfeld, M.S.P. Sansom, O. Beckstein,
Lipidbook: a public repository for force-field parameters used in membrane simulations,
J. Membr. Biol. (2010) 255-8
A powerful web-tool helping scientists be more creative
An extension to molecular dynamics codes for running enhanced sampling simulations
Link to contributions
A public repository for OPLS-AA ligand parameters.
Older brother to ligandbook.
A top-notch MD data analysis library. Link to contributions
A "Sargasso Sea" of assorted notes, unfinished projects.