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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 2005.

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Dr. Matthew Wright

Product Director


Molecule and Markush Structure Analysis within Oracle

digital chemistry
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 chemistry1
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 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
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 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 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











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
torus patent prototype demo
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
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
Result viewing
  • Results of the query show patent structure along with the original patent in PDF format in a list
result viewing1
Result viewing
  • Patent chemistry structures can also be displayed. A viewer is available which allows easy viewing of all Markush core/R-Group members

Markush core(s)

Tree view of Markush structure

R-Group members

result viewing2
Result viewing
  • The original PDF of each result patent can be viewed directly from Torus:View
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