Journal
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
Volume 29, Issue 2, Pages 157-170Publisher
ELSEVIER SCIENCE INC
DOI: 10.1016/j.jmgm.2010.05.008
Keywords
2D fingerprint; Similarity searching; Enrichment; Scaffold hopping; Ligand-based virtual screening; Virtual screening
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Virtual screening is a widely used strategy in modern drug discovery and 20 fingerprint similarity is an important tool that has been successfully applied to retrieve active compounds from large datasets. However, it is not always straightforward to select an appropriate fingerprint method and associated settings for a given problem. Here, we applied eight different fingerprint methods, as implemented in the new cheminformatics package Canvas, on a well-validated dataset covering five targets. The fingerprint methods include Linear, Dendritic, Radial, MACCS, MOLPRINT2D, Pairwise, Triplet, and Torsion. We find that most fingerprints have similar retrieval rates on average; however, each has special characteristics that distinguish its performance on different query molecules and ligand sets. For example, some fingerprints exhibit a significant ligand size dependency whereas others are more robust with respect to variations in the query or active compounds. In cases where little information is known about the active ligands, MOLPRINT2D fingerprints produce the highest average retrieval actives. When multiple queries are available, we find that a fingerprint averaged over all query molecules is generally superior to fingerprints derived from single queries. Finally, a complementarity metric is proposed to determine which fingerprint methods can be combined to improve screening results. (C) 2010 Elsevier Inc. All rights reserved.
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