2D-Structure Drawings of Similar Molecules
A common strategy in drug design and pharmacophore identification consists of evaluating large sets of molecular structures by comparing their 2D structure drawings. To simplify the chemists’ task, the drawings should reveal similarities and differences between drugs. Given a family of molecules all containing a common template, we present an algorithm to compute standardised 2D structure drawings. The molecules being represented as a graph, we compute a structure called supertree in which all molecules can be embedded. Using the correspondences between atoms provided by the supertree, we are able to coordinate the drawings performed by a breadth-first traversal of the molecular graphs. Both parts of the problem are NP-hard. We propose algorithms of heuristic nature.
- 1.Tatsuya Akutsu and Magnús M. Halldórsson. On the approximation of largest common subtrees and largest common point sets. Theoretical Computer Science, to appear 2000.Google Scholar
- 2.Jean-Daniel Boissonnat, Fréderic Cazals, and Julia Flötotto. 2d-structure drawings of similar molecules. Technical report, INRIA Sophia Antipolis, to appear 2000.Google Scholar
- 4.F. Cazals. Effective nearest neighbours searching on the hyper-cube, with applications to molecular clustering. In 14th ACM Symposium on Computational Geometry, pages 222–230, 1998.Google Scholar
- 5.G. di Battista, P. Eades, R. Tamassia, and I. Tollis. Graph Drawing. Prentice Hall, 1999.Google Scholar
- 8.R. J. Feldmann, S. R. Heller, E. Hyde, and W. T. Wipke (Ed.). Computer Representation and Manipulation of Chemical Information, pages 55–60. Wiley, New York, 1974.Google Scholar
- 11.M. Himsolt. Gml: A portable graph file format. Technical report, Universität Passau, 1997. cf. http://www.fmi.uni-passau.de/himsolt/Graphlet/GML.
- 12.D. R. Musser and Atul Saini. STL Tutorial and Reference Guide. Addison-Wesley Publishing Company, 1995.Google Scholar
- 13.V. Nicholson, C.-C. Tsai, M. Johnson, and M. Naim. A subgraph isomorphism theorem for molecular graphs. In Graph theory and topology in chemistry, Collect. Pap. Int. Conf., volume 51 of Stud. Phys. Theor. Chem., pages 226–230, Athens/GA, 1987.Google Scholar
- 15.J. van Leeuwen (Ed.). Handbook of Theoretical Computer Science, volume A. Elsevier, 1990.Google Scholar