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J Comput Aided Mol Des. 2009 Apr;23(4):253-9. doi: 10.1007/s10822-008-9255-y. Epub 2008 Dec 10.

ChemGPS-NP(Web): chemical space navigation online.

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Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, BMC Box 574, 75123 Uppsala, Sweden.


Internet has become a central source for information, tools, and services facilitating the work for medicinal chemists and drug discoverers worldwide. In this paper we introduce a web-based public tool, ChemGPS-NP(Web) (, for comprehensive chemical space navigation and exploration in terms of global mapping onto a consistent, eight dimensional map over structure derived physico-chemical characteristics. ChemGPS-NP(Web) can assist in compound selection and prioritization; property description and interpretation; cluster analysis and neighbourhood mapping; as well as comparison and characterization of large compound datasets. By using ChemGPS-NP(Web), researchers can analyze and compare chemical libraries in a consistent manner. In this study it is demonstrated how ChemGPS-NP(Web) can assist in interpreting results from two large datasets tested for activity in biological assays for pyruvate kinase and Bcl-2 family related protein interactions, respectively. Furthermore, a more than 30-year-old suggestion of "chemical similarity" between the natural pigments betalains and muscaflavins is tested.

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