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Digital Chemistry
• Company, formed Mid-2005• Acquired Barnard Chemical Information
(BCI) September 2005. – 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 :
R1
*Br
*ClR1=
R1
*Cl
*BrR2=
*O
R2 *N
R2R1=
R1
R2
* 'O
* '' * 'N
* ''R1 + R2 =
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)• (CH2) repeats m times
– Position variation (p-variation)• R2 has a number of attachment points
– Homology variation (h-variation)• R3 is Alkyl, Methyl
R1
R3
(CH2)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
Contact Us
www.digitalchemistry.co.uk
+44 (0)113 2181850
The Iron Shed, Harewood House Estate,Leeds, LS17 9LF, United Kingdom