Visual exploration of structure-activity relationship using maximum common framework

J Comput Aided Mol Des. 2008 Aug;22(8):571-8. doi: 10.1007/s10822-008-9206-7. Epub 2008 Mar 13.


To help tracking all molecules made in a typical medicinal chemistry project, we have developed an algorithm to generate a maximum common framework (MCF) hierarchy and an interactive tool for its visualization and analysis. By identifying all unique frameworks for a set of molecules and all molecules containing each framework, we were able to simplify the MCF hierarchy build up steps and, as a result, speed up the entire process significantly. By allowing compounds to be assigned to multiple MCFs, users can easily remove bad branching nodes and concentrate on interesting ones. MCF hierarchies provide an effective and intuitive visualization for tracking medicinal chemistry lead optimization projects. We will provide examples to illustrate its usefulness.

MeSH terms

  • Algorithms*
  • Chemistry, Pharmaceutical / methods
  • Molecular Structure
  • Naphthalenes / chemistry
  • Pharmaceutical Preparations / chemistry*
  • Protein Kinase Inhibitors / chemistry
  • Pyrazoles / chemistry
  • Software
  • Software Design
  • Structure-Activity Relationship
  • User-Computer Interface*


  • BIRB 796
  • Naphthalenes
  • Pharmaceutical Preparations
  • Protein Kinase Inhibitors
  • Pyrazoles