Comparison of topological descriptors for similarity-based virtual screening using multiple bioactive reference structures

Org Biomol Chem. 2004 Nov 21;2(22):3256-66. doi: 10.1039/B409865J. Epub 2004 Sep 29.


This paper reports a detailed comparison of a range of different types of 2D fingerprints when used for similarity-based virtual screening with multiple reference structures. Experiments with the MDL Drug Data Report database demonstrate the effectiveness of fingerprints that encode circular substructure descriptors generated using the Morgan algorithm. These fingerprints are notably more effective than fingerprints based on a fragment dictionary, on hashing and on topological pharmacophores. The combination of these fingerprints with data fusion based on similarity scores provides both an effective and an efficient approach to virtual screening in lead-discovery programmes.

Publication types

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

MeSH terms

  • Algorithms*
  • Chemistry, Pharmaceutical / methods
  • Computer Simulation
  • Databases, Factual*
  • Drug Design
  • Drug Evaluation, Preclinical / methods*
  • Pharmaceutical Preparations*
  • Quantitative Structure-Activity Relationship*


  • Pharmaceutical Preparations