Chemical Database Engine Speeds Searching of Large Virtual Libraries

Used by more than 80 percent of life sciences organisations worldwide, the cartridge offers proven performance with databases containing over 17 million reactions and over 30 million structures.

The new Markush functionality in Symyx Direct supports combinatorial library design and patent claim analysis in drug discovery by greatly expanding the techniques available for managing and exploring large numbers of related chemical substructures. A Markush structure represents a large number of compounds as a single, generic entry by identifying a core structure and listing all possible variants or substitutes using Rgroup notations and substituent lists. Markush structures make it possible to generate and index all possible permutations of a specific chemical entity without creating an unmanageable information repository.

"The ability of Symyx Direct 6.3 to handle substructure and exact match queries using both discrete and Markush structures makes it an indispensable application for scientists attempting to capture, represent or protect regions of related chemical structure space," said Dr. Trevor Heritage, president of Symyx's software business unit. "The addition of generic structure searching and overlap analysis makes it possible for scientists to analyse the diverse chemistry that Markush technology can represent."

The Symyx Direct chemistry cartridge is a central component of the chemistry engine underlying Symyx Notebook, Symyx Isentris® and related scientific workflow applications including Symyx Registration software.

The Symyx Direct cartridge supports Rgroup, Sgroup, flexmatch, 2-D and 3-D exact and molecule substructure searching; structure similarity searching; reaction similarity searching; searching of tetrahedral stereoisomers and non-tetrahedral stereoisomers; storage and retrieval of sequences including peptides, oligonucleotides and oligosaccharides-and now Markush structure storage, searching and retrieval.