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Nina M. Fischer

  • Since 2007 PhD student in Oliver Kohlbacher's group (Applied Bioinformatics), Dept. of Computer Science, Eberhard Karls University Tübingen, Germany.
  • October - December 2006 Visitor in Boris Lenhard' group at CBU, which is part of the Bergen Center for Computational Science at the University of Bergen, Norway.
  • 2006 Diploma Thesis - Structure-based prediction of transcription factor-DNA binding free energies using MM/GBSA - in Oliver Kohlbacher's group.
  • 2003-2006 Eberhard Karls University Tübingen, Computational Biology (Diploma in Computer Science / Computational Biology).
  • 2002-2003 Western Michigan University, Kalamazoo, USA, Computer Science/Biochemistry.
  • 2000-2002 Eberhard Karls University Tübingen, Computational Biology.
  • In 2000 High school graduation.


Research Interests:

  • Protein-DNA complexes: Structural modeling of protein-DNA complexes for exploring protein-DNA interactions at the binding interface using molecular dynamics (MD) simulations.

  • Flexible proteins and protein-ligand complexes: Studying protein-ligand interactions using flexible receptor docking and clustering approaches as well as molecular dynamics (MD) simulations and PCA.


Selected Publications and Posters:

  • Fischer, N.M., Kohlbacher, O., The Analysis of Cis-elements: Current developments, knowledge and application to gene networking, Chapter 13: Structural insights into physical interactions of transcription factor-DNA complexes at an atomic level. (submitted in 2011) [e-book chapter]

  • Wanke, D., Brand, L.H., Fischer, N.M., Peschke, F., Kilian, J., and Berendzen K.W., Implications of DNA-nanostructures by Hoogsteen-dinucleotides on transcription factor binding. In: WSPC – Proceedings (submitted in 2011) [book chapter]

  • Fischer, N.M., Wanke, D., Kohlbacher, O., Shedding light on transcription factor binding sites using MD. Hünfeld 2009 Workshop on Computer Simulation and Theory of Macromolecules [poster]

  • Fischer, N.M., Schneider, W.M, Kohlbacher, O., Rescoring of docking poses using force field based methods. J Cheminform. 2010; 2(Suppl 1):P52, published online May 2010. GCC 2009 [poster]

  • Fischer, N.M., Höglund A., Kohlbacher, O., Structure-based prediction of transcription factor-DNA binding free energies using MM/GBSA. ISMB/ECCB 2007 [poster]

Latest content created by this user

Page
Talks Sep 24, 2009
Inhalte Apr 10, 2012
Studentenseminar Apr 19, 2011
Software May 02, 2012
Inhalte Apr 10, 2012
File
Uebung06.pdf Jun 06, 2012
NW.py Jun 06, 2012
09. Protein Structure Prediction - Part I (Handout) Jun 05, 2012
09. Protein Structure Prediction - Part I Jun 05, 2012
08. Modeling of Proteins - Part III (Handout) May 21, 2012
Folder
BILS Jan 30, 2012
ASDD Aug 17, 2010
Übungsblätter Apr 10, 2012
Folien Apr 10, 2012
Software May 02, 2012
Image
kinase Sep 12, 2013
kinase Sep 25, 2012
kinase Aug 22, 2011
kinase Aug 22, 2011
kinase Aug 17, 2010
All content created by Nina M. Fischer…