Selecting diversified compounds to build a tangible library for biological and biochemical assays.

Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry
Qiong GuLianquan Gu

Abstract

The quality of diverse compound selection mainly depends on cluster algorithms, descriptors, the combinations of the descriptors, and similarity metrics. The Jarvis-Patrick algorithm, MDL search keys, and Daylight fingerprints are a well accepted algorithm and structure descriptors for compound library diversity analysis. Based upon our 288 experiments on selecting compounds from various descriptor combinations, we have found (1) hybrid Daylight and MDL structural descriptors for diversity analyses can produce worse results; (2) selections based purely on 2,048-bit Daylight fingerprints yield better results than the ones based purely on MDL 166-bit search keys; (3) when Daylight fingerprints and MDL search keys are combined, it is better to compute the similarities independently, then to take the smaller value for the outcome. This will yield better average separation of clusters; (4) regarding the consistency of different clustering approaches, the Daylight fingerprints based clustering is more consistent with the SCA approach than it does with the MDL search keys based approach; (5) The MDL search keys based selection approach tends to select a greater number of compounds from larger clusters. As the Daylight fingerprint is f...Continue Reading

References

Jan 5, 2002·Journal of Medicinal Chemistry·Olivier RocheGisbert Schneider
Nov 15, 2002·Journal of Medicinal Chemistry·Jun Xu
Nov 26, 2002·Journal of Chemical Information and Computer Sciences·Joseph L DurantJames G Nourse
Feb 5, 2003·Drug Discovery Today·Gilbert M Rishton
Apr 4, 2003·Journal of Medicinal Chemistry·Susan L McGovern, Brian K Shoichet
Sep 19, 2003·Journal of Medicinal Chemistry·Susan L McGovernBrian K Shoichet
Oct 3, 2003·Journal of Medicinal Chemistry·James SeidlerBrian K Shoichet
Mar 31, 2006·Journal of Medicinal Chemistry·Brian Y Feng, Brian K Shoichet
Jun 24, 2006·Drug Discovery Today·Brian K Shoichet
Apr 24, 2007·Journal of Medicinal Chemistry·Brian Y FengChristopher P Austin

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Citations

Jul 19, 2011·Journal of Chemical Information and Modeling·Vincent Le GuillouxLuc Morin-Allory
Aug 26, 2010·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Ibrahim TumenMarkku Reunanen

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Software Mentioned

MOE
Windows
Visual C + +
SCA
Daylight

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