Kristoffer Enøe Johansson

Kristoffer Enøe Johansson

Akademisk medarbejder FU

  • Education

Department of Biology, University of Copenhagen, 18 Dec 2012

Cand.scient .  Niels Bohr Institute, University of Copenhagen, 15 Aug 2006

  • Educational Board of Nanotechnology, Jan 2003–Jun 2005

 

Teaching

Structural Bioinformatics, fall 2009, 2010 and 2011. I planned and executed the computational exercise classes for ∼20 bioinformatics master students with backgrounds ranging from biology to computer science.  English language.

 

Employment

Postdoc Dept. of Pharmacy, UCPH, Jun 2013–May 2016

  • In the Computational Materials Science group, Section of Pharmaceutical Technol- ogy and Engineering, Department of Pharmacy, University of Copenhagen I work with molecular dynamics simulations and tailor-made force fields based on DFT cal- culations.

 Research Assistant Dept. of Biology, UCPH, Jun 2012–Jul 2012

  • In the group of Jakob R. Winther, Section for Biomolecular Sciences, Department of Biology, University of Copenhagen I did a computational redesign of the redox protein thioredoxin for academic purposes.

Ph. D. Student Dept. of Biology, UCPH, Feb 2009–Maj 2012

  • The position covered the computational branch of a protein design project based on available state-of-the-art methods. In addition, I developed novel methods for Monte Carlo based simulation of protein structure and design.

 Staff Scientific at DFM, Sep 2008–Dec 2008

Danish Fundamental Metrology (DFM) is the Danish national metrology institute. DFM develops and maintains national standards within mass, electricity and acous- tics among others. As an employee in a time limited position in the length and nano section, I developed software for analyzing AFM measurements of 1D gratings.

  

  

 Publications:

  •  Xiaozhou Li, Andrew D. Bond, Kristoffer E. Johansson and Jacco van de Streek: ’Distinguishing  tautomerism  in  the  crystal  structure  of  (Z)-N-(5-ethyl-2,3-dihydro- 1,3,4-thiadiazol-2-ylidene)-4-methylbenzenesulfonamide using DFT-D calculations and 13C solid-state NMR’, Acta Crystallographica C70, p 784 (2014).
    Kristoffer E. Johansson and Thomas Hamelryck: ’A Simple Probabilistic Model of Multibody Interactions in Proteins’, Proteins: Structure, Function, and Bioinfor- matics 81, p 1340 (2013).
  •  Wouter Boomsma, Jes Frellsen, Tim Harder, Sandro Bottaro, Kristoffer E. Johans- son, Pengfei Tian, Kasper Stovgaard, Christian Andreetta, Anders S. Christensen, Simon Olsson, Jan Valentin, Mikael Borg, Jesper Ferkinghoff-Borg and Thomas Hamelryck: ’PHAISTOS: A Framework for Markov Chain Monte Carlo Simulation of Proteins’, Journal of Computational Chemistry 34, p 1697 (2013).
  • Sandro Bottaro, Wouter Boomsma, Kristoffer E. Johansson, Christian Andreetta, Thomas Hamelryck and Jesper Ferkinghoff-Borg: ’Subtle Monte Carlo updates in dense molecular systems’, Journal of Chemical Theory and Computation, 8, p 695 (2012).
  •  Tim Harder, Wouter Boomsma, Martin Paluszewski, Jes Frellsen, Kristoffer E. Jo- hansson and Thomas Hamelryck: ’Beyond rotamers: A generative, probabilistic model of side chains in proteins’, BMC Bioinformatics 11, p 306 (2010).
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Software

 

Developer on Phaistos. Phaistos is a framework for Markov chain Monte Carlo simulation and inference of protein structure written in C++. I have contributed an implementation of the OPLS-AA/L all atom force field and the probabilistic MuMu model of non-local interactions in proteins.

ID: 11048943