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.
Publications
-
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
https://doi.org/10.1016/j.str.2018.05.003
-
J. Domański, M.S.P. Sansom, P.J. Stansfeld, R.B. Best,
Balancing Force Field Protein–Lipid Interactions To Capture Transmembrane Helix–Helix Association
https://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00983
-
J. Domański, O. Beckstein, B. Iorga,
Ligandbook - an online repository for small and drug-like molecule force field parameters
https://www.ncbi.nlm.nih.gov/pubmed/28130228
-
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
DOI: 10.1021/acs.jpcb.6b08445
-
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
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.P. Sansom, O. Beckstein,
Lipidbook: a public repository for force-field parameters used in membrane simulations,
J. Membr. Biol. (2010) 255-8
20700585
Other work
Labstep
A powerful web-tool helping scientists be more creative
Plumed
An extension to molecular dynamics codes for running enhanced sampling simulations
Link to contributions
Ligandbook
A public repository for OPLS-AA ligand parameters.
Lipidbook
Older brother to ligandbook.
MDAnalysis
A top-notch MD data analysis library. Link to contributions
Technical blog
A "Sargasso Sea" of assorted notes, unfinished projects.