Scaffold Hunter - A tool for the visual analysis and exploration of chemical space

The challenging task in Cheminformatics is to support the drug discovery process by adequate computational methods including largely automated data mining algorithms as well as visual analysis tools. Our research includes algorithms to compare graphs, which are a prerequisite to apply data mining algorithms to structured objects like chemical compounds. Moreover, we develop methods for searching graph databases as well as visual analysis approaches for chemical space.

We develop Scaffold Hunter, a tool for the analysis and exploration of chemical space aiming at an intuitive access to large and complex data sets. The tool offers a variety of views, e.g. graph, dendrogram, and plot view, as well as analysis methods, e.g., for clustering and classification.


  • Explicit versus Implicit Graph Feature Maps: A Computational Phase Transition for Walk Kernels
    Nils Kriege, Marion Neumann, Kristian Kersting, Petra Mutzel
    International Conference on Data Mining (ICDM) 2014, to appear.
  • On Maximum Common Subgraph Problems in Series-Parallel Graphs
    Nils Kriege, Florian Kurpicz, Petra Mutzel
    International Workshop on Combinatorial Algorithms (IWOCA) 2014, to appear.
  • The Landscape Metaphor for Visualization of Molecular Similarities
    Martin Gronemann, Michael Jünger, Nils Kriege, Petra Mutzel
    in: Battiato, S.; Coquillart, S.; Laramee, R. S.; Kerren, A. & Braz, J. (Eds.), Computer Vision, Imaging and Computer Graphics. Theory and Application; Communications in Computer and Information Science, 2014, 458, 85-100.
  • Scaffold Hunter: Visual Analysis of Biological Activity Data
    Karsten Klein, Oliver Koch, Nils Kriege, Petra Mutzel, Till Schäfer
    German Conference on Chemoinformatics, Fulda, Germany, 2013.


  • Effiziente Enumerationsalgorithmen für Common Subtree Probleme
    Andre Droschinsky, Diploma Thesis, 2014
  • Efficient algorithms for the maximum common subgraph problem in partial 2-trees
    Florian Kurpicz, Master Thesis, 2014
  • Verfeinerung bitvektorbasierter Filterverfahren zur Substruktursuche in Molekülgraphdatenbanken
    Fabian Weißberg, Bachelor Thesis, 2013
  • Beschleunigung hierarchischer Clusterverfahren für allgemeine metrische Distanzmaße
    Till Schäfer, Diploma Thesis, 2012
  • Entwurf von Oligonukleotid-Bibliotheken für die DNA-Nanotechnologie
    Marianna D'Addario, Diploma Thesis, 2011 (Collaboration with Prof. Rahmann and Prof. Niemeyer, Chemistry)
Last modified: 2015-09-11 13:18 (external edit)