Magnus Lundborg


Since June 2015 I am working for the company ERCO Läkemedel AB modelling the lipid matrix of stratum corneum in skin. I still work at the same location as, and together with, Erik Lindahl’s group at SciLifeLab. My personal main interest is molecular modelling methods for use in medicinal chemistry.

Molecular dynamics simulations have a large potential in drug development. Binding free energies can, (in theory) be calculated accurately and the interaction process can be studied in detail. There are still hurdles to complicate the process. Firstly, it is not trivial to properly generate topologies of generic small molecules and the force field parameters themselves do not always give accurate results. It can also take a long time to perform the calculations, even with good computers at hand.

I am trying to simplify the process of topology generation for different force fields for GROMACS. STaGE generates topologies of small molecules and is available using git: “git clone”. Using Copernicus, the solvation and binding free energy calculations can be conveniently distributed over a network and the results collected afterwards. Force field parameters will soon be looked at and possibly tweaked to improve the results.

Molecular docking can be used to elucidate how and where small molecules interact with proteins. In general, docking programs are good at generating poses, but not as good at calculating binding free energies or ranking molecules according to their fit with the protein. Combining docking with MD simulations can improve this, but requires a convenient work flow.

In addition to this I have been developing the TNG file format for efficient storage of trajectories from MD simulations.

I also have a background in NMR analysis of carbohydrates and also developing tools for fragment-based NMR screening.

See also my LinkedIn profile.

Selected Publications

See Google Scholar Citations for publication list.


2015- Molecular modeller, ERCO Läkemedel AB, Science for Life Laboratory.

2015-2015 Structural bioinformatician, BILS, Science for Life Laboratory.

2012-2015 Postdoctoral researcher, Science for Life Laboratory, Department of Theoretical Physics, KTH/Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.

2011-2012 Postdoctoral researcher, Department of Biochemistry, University of Cambridge, Cambridge, UK.

2006-2011 PhD student, Department of Organic Chemistry, Stockholm University, Stockholm, Sweden.

1999-2005 MSc Pharmaceutical Chemistry, Uppsala University, Uppsala, Sweden.