Visualizing high dimensional descriptors of molecular structures

Abstract

The distribution of chemical compounds in high-dimensional molecular descriptor space can be viewed in two dimensions by applying the projection method of this invention. This method has particular usefulness for viewing the relationships of a large number of compounds such as found in a large scale HTS or virtual combinatorial library. After selecting a representative subset of the larger data set of compounds, initially components from the high-dimensional descriptor space are determined by PCA. In order to relax an NLM projection using the PCA components as a start, the stress function is modified to reflect a local horizon beyound which the separation of the compounds is not meaningfully measureable. The resulting two dimensional projections provide a clear insight into the distribution of the chemical compounds in the higher dimensional space. The method is clearly generalizable to viewing descriptor space in three dimensions and to using high dimensional descriptors other than those used to describe molecular structure.

Description

[0001] A computer program listing appendix is part of the disclosure and is incorporated herein by reference. The computer program listing appendix contained on compact disks contains the following files: Identification Information (1 KB) and NLMJER.C (20 KB). The disks were created on Oct. 27, 2003.

[0002] A portion of the disclosure of this patent document contains material which is subject to copyright protection. The copyright owner has no objection to the facsimile reproduction by anyone of the patent document or the patent disclosure, as it appears in the Patent and Trademark Office patent file or records, but otherwise reserves all copyright rights whatsoever.

[0003] 1. Field of the Invention

[0004] This invention relates to the field of computational molecular structural analysis of large data sets of molecular structures and more specifically to graphical displays that present an accurate qualitative representation of the distribution of molecular structures in the high dimens...

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