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Research Article

New Diversity Calculations Algorithms Used for Compound Selection

Sergei V. Trepalin,*^† Vadim A. Gerasimenko,^† Andrey V. Kozyukov,^‡ Nikolay Ph. Savchuk,^‡ and Andrey A. Ivaschenko^‡

Institute of Physiologically Active Compounds, 142432 Chernogolovka, Moscow Region, Russia, and ChemDiv, Inc. 11575 Sorrento Valley Road, #210, San Diego, California 92121

J. Chem. Inf. Comput. Sci., 2002, 42 (2), pp 249–258

DOI: 10.1021/ci0100649

Publication Date (Web): February 1, 2002

Corresponding author phone: (096)524-8269; e-mail: Sergey_ Trepalin@chemdiv.com; trep@ism.ac.ru.

†

Institute of Physiologically Active Compounds.

‡

ChemDiv, Inc.

Abstract

Some modifications were introduced into the previously described Centroid diversity sorting algorithm, which uses cosine similarity metric. The modified algorithm is suitable for the work with large databases on personal computers. For example, for diversity sorting of the database with the size greater than a million of records, less than 9 h are required (Pentium III, 800 MHz). The problem of selecting new compounds into the existing collection is examined to reach the maximum diversity of the collection. The article describes the new algorithm for the selection of heterocyclic compounds.

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