Development and validation of AMANDA, a new algorithm for selecting highly relevant regions in Molecular Interaction Fields

J Chem Inf Model. 2008 Sep;48(9):1813-23. doi: 10.1021/ci800037t. Epub 2008 Aug 12.


Descriptors based on Molecular Interaction Fields (MIF) are highly suitable for drug discovery, but their size (thousands of variables) often limits their application in practice. Here we describe a simple and fast computational method that extracts from a MIF a handful of highly informative points (hot spots) which summarize the most relevant information. The method was specifically developed for drug discovery, is fast, and does not require human supervision, being suitable for its application on very large series of compounds. The quality of the results has been tested by running the method on the ligand structure of a large number of ligand-receptor complexes and then comparing the position of the selected hot spots with actual atoms of the receptor. As an additional test, the hot spots obtained with the novel method were used to obtain GRIND-like molecular descriptors which were compared with the original GRIND. In both cases the results show that the novel method is highly suitable for describing ligand-receptor interactions and compares favorably with other state-of-the-art methods.

Publication types

  • Research Support, Non-U.S. Gov't
  • Validation Study

MeSH terms

  • Algorithms*
  • Binding Sites
  • Computer Simulation*
  • Drug Design*
  • Imaging, Three-Dimensional
  • Ligands
  • Models, Chemical*
  • Models, Molecular
  • Molecular Structure
  • Pharmaceutical Preparations / chemistry
  • Quantitative Structure-Activity Relationship


  • Ligands
  • Pharmaceutical Preparations