Dr. Matthew Wright Product Director

Torus Molecule and Markush Structure Analysis within Oracle

Digital Chemistry Company, formed Mid-2005 Acquired Barnard Chemical Information (BCI) September –All previous BCI directors and staff are now employed by Digital Chemistry. Aim to build on top of existing BCI technology and know-how, predominantly their Markush and Clustering methods Now moving into patent space

Digital Chemistry Product range covering –Cluster/diversity analysis –Markush library analysis –Chemical fingerprinting and dictionaries –Structure query conversion (MDL > Daylight) Software distributed as –Toolkits (C, C++, Java, Perl, Python) –Web Services –Application suites

Torus overview Torus:Server –Oracle based cartridge which integrates both Molecule and Markush structure storage and retrieval –SQL based interface, but Query can be supplied from SMARTS, ISIS/Draw or ChemDraw –Client may be Torus:View or any SQL supporting application, e.g. PipeLine Pilot or customer developed system due to open nature of SQL interface Torus:View –Optional client for Torus:Server. Allows searching of Torus:Server database with graphical display of results.

Markush Structures Presently within Torus:Server Markush structures have attachments defined in a number of ways (with unlimited members), including : Simple substitution : Nested R-Groups : Bridged R-Groups :

Torus: Server Function summary #1 Torus:Server supports a number of SQL based functions: Structural equivalence check –Are two libraries/molecules equivalent Sub-structure/Exact-structure searching –Into Mol and Markush Overlap between Markush libraries –Also produce third Markush representing overlap Similarity –Of molecule into Markush and between two Markush libraries Property calculation, both in molecule and Markush –Supports all Lipinski rules, e.g. weight, LogP etc

Torus: Server Function summary #2 Torus:Server supports a number of SQL based functions: Markush enumeration –Typical enumeration speeds > 100k structures per second Query format conversion –MDL MOL/SKC to Daylight SMARTS Miscellaneous utility functions

Markush Structures – current work Currently support substituent variation (s-variation) – useful for combinatorial chemistry Current and future work extends the Markush representation to cover further generalisations leading to a full Markush structure search for use in Patent systems: –Substituent variation (s-variation) R1 can have a number of substitutions –Frequency variation (f-variation) (CH 2 ) repeats m times –Position variation (p-variation) R2 has a number of attachment points –Homology variation (h-variation) R3 is Alkyl, Methyl R1 R3 (CH 2 ) m R2 H

Torus:Patent prototype demo Live demonstration based up Thomson patent data, all data held on laptop Schema contains patent PDF, patent ID and patent Markush structures Database covers 8,709,704,764,382,349 specific compounds if enumerated Oracle/Torus:Patent server running on laptop

Query creation Queries against Torus:Patent database are easily drawn in ISIS/Draw (supporting all ISIS Query features) and transferred back into Torus:View ready for query against the patent database in Torus:Patent

Result viewing Results of the query show patent structure along with the original patent in PDF format in a list

Result viewing Patent chemistry structures can also be displayed. A viewer is available which allows easy viewing of all Markush core/R-Group members Tree view of Markush structure Markush core(s) R-Group members

Result viewing The original PDF of each result patent can be viewed directly from Torus:View

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