Dr. Anna-Katharina Hildebrandt
July 27, 2012 2023-11-10 11:17Dr. Anna-Katharina Hildebrandt
Researcher
Contact
Center for Bioinformatics
Saarland Informatics Campus
Saarland University
Building E2.1, Room 402
P.O. Box 15 11 50
66041 Saarbrücken
Germany
Research
My current research interests are in the fields of structure based bioinformatics and eLearning:
- NMR-based structure analysis and docking algorithms (Drug Design and Machine Learning)
- Real time ray tracing techniques in Molecular Visualization for the molecular viewing and editing tool BALLView
- Optimization techniques, e.g., for bond order assignment (Cheminformatics)
- Computational Proteomics
- Image Processing
- The BALL project
- Development of web interfaces for bioinformatic services (ballaxy)
- Bioinformatics education, e.g. MSWissenschaft
- computational proteomics
Education
- since 04/2012: Postdoctoral researcher at chair of Prof. Lenhof, Center for Bioinformatics
- 03/2012: PhD-thesis at Graduate School of Saarland University, chair of Prof. Lenhof, Center for Bioinformatics
- 04/2007: Master’s Degree, Saarland University
- 10/2005: Bachelor’s Degree, Saarland University
- 2004: Summer placement at the Bioinformatics Research Center at Glasgow University
- 2002-2007: Studies in Computational Biology at Saarland University
- 1999-2002: Job training as Mathematisch-Technische Assistentin/Informatik (IHK) at AXA Tech
Teaching
- TA Bioinformatics 1 (WS 07/08, WS 08/09, WS 09/10, WS 10/11, WS 11/12, WS 12/13, WS 13/14)
- TA Bioinformatics 2 (SS 06, SS 07, SS 09, SS 11, SS 12, SS 13)
- TA “Fighting Cancer in Bioinformatics”(SS 08)
- Proseminar “Bioinformatic Approaches for Cancer Research” (repeatedly 2007-2013)
- Proseminar “Efficient Algorithms for RNA molecules” (repeatedly 2007-2013)
- Seminar “Modelling and Analyzing Biological Networks” (repeatedly 2007-2013)
- Seminar “Selected Topics in Molecular Docking” (repeatedly 2007-2013)
- Seminar “Computation in Systems Biology” (WS 07/08)
- Girl’s Day / Girl’s Camp (SS07, SS 08, SS09, WS 09/10)
- “Implementation of RNA shift prediction in BALL” (Christina Kiefer WS13/14)
- “XML3D based molecular structure visualization using BALLView and BALLaxy” (Lukas Brausch WS13/14)
- “Segmentation of biological images based on space and colour neighbourhood” (Sebastian Schattner, SS13)
- “Normal Mode Based Structure Recognition for Scoring Cryo-EM Images” (Vanessa Morguet, SS13)
- “Erweiterung und Evaluierung von BALLView und des Präsentationsframeworks PresentaBALL für den Einsatz im Chemieunterricht an weiterführenden Schulen” (Markus Konietzko, SS12)
- “Design and implementation of the functionality to align sequences and structures into the Biochemical Algorithms Library” (Nikola Koch, SS12)
- “Implementation of a Graph Coloring Algorithm for InChi Computation” (Alexander Zapp, SS12)
- “pKa-dependent Bond Order Assignment of Organic Molecules” (Adrian Fritz, WS11/12)
- “Statistical Analysis of Bond Orders in Ligand Molecules” (Alexander Gress, SS12)
- “A hybrid model for NMR chemical shift prediction” (Simon Loew, WS10/11)
- “Structural Stability and Immunogenicity of Peptides” (Eva Kranz, WS09/10)
- “TNF alpha antibody design” (Miriam Mangels , WS09/10)
Latest Publications
[DOT+15] Dietzen, M., Kalinina, O.V., Taskova, K., Kneissl, B., Hildebrandt, A.-K., Jaenicke, E., Decker, H., Lengauer, T., and Hildebrandt, A.:Large oligomeric complex structures can be computationally assembled by efficiently combining docked interfaces. Proteins: Structure, Function, and Bioinformatics. 2015
[HSH+15] Hoang-Vu, D., Schmidt, B., Hildebrandt, A., Tran, T.T. and Hildebrandt, A.-K: CUDA-enabled hierarchical ward clustering of protein structures based on the nearest neighbour chain algorithm International Journal of High Performance Computing Applications, 2015
[AKH+14] Hildebrandt, A. K., Stöckel D., Fischer, N. M., de la Garza, L., Krüger, J., Nickels, S., Röttig, M., Schärfe, C., Schumann, M., Thiel, P., Lenhof, H.-P., Kohlbacher, O., and Andreas Hildebrandt, ballaxy: web services for structural bioinformatics, Bioinformatics 2014, doi: 10.1093/bioinformatics/btu574
[HDL+14] Hildebrandt, A.K., Dietzen, M., Lengauer, T., Lenhof, H.-P., Althaus, E., and Hildebrandt, A. Efficient computation of root mean square deviations under rigid transformations. J Comput Chem. 35(10):765–771, 2014
[AHH14] Althaus, E., Hildebrandt, A. and Hildebrandt, A.K. A Greedy Algorithm for Hierarchical Complete Linkage Clustering. 1st International Conference on Algorithms for Computational Biology (AlCoB 2014)
International Conferences
Predicting Protein NMR Chemical Shifts in the Presence of Ligands and Ions using Force Field-based Features. At: German Conference on Bioinformatics, 8. September 2011, Weihenstephan, Germany
A Pipeline for the training of NMR chemical shift prediction models. At: 25th Molecular Modelling Workshop 2011, 4. April 2011, Erlangen, Germany
Automated Bond Order Assignment as an Optimization Problem. At: German Conference on Bioinformatics, 30. September 2009, Halle, Germany
Discrete Optimization Techniques for Optimal Bond Order Assignment. At: JCB Seminar, Chair of Prof. Sebastian B¨ocker, 4. December 2008, Jena, Germany
Awards
- Arts and Science Award of ECCB/ISMB 2011 Vienna
- Best poster award at GCB 2009 (German Conference on Bioinformatics,Halle (Saale), Germany, 28-30 Sep 2009)
- Best poster award at 1st PhD student day Life-science Saarland University,Germany, 2009
