1 / 15

digitalchemistry.co.uk

Dr. Matthew Wright Product Director. www.digitalchemistry.co.uk. Torus. Molecule and Markush Structure Analysis within Oracle. Digital Chemistry. Company, formed Mid-2005 Acquired Barnard Chemical Information (BCI) September 2005.

hilda-hewitt
Download Presentation

digitalchemistry.co.uk

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Dr. Matthew Wright Product Director www.digitalchemistry.co.uk

  2. Torus Molecule and Markush Structure Analysis within Oracle

  3. 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

  4. 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

  5. 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.

  6. 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 :

  7. 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

  8. 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

  9. R1 H ( C H ) m 2 R3 R2 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

  10. 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

  11. 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

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

  13. 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

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

  15.    www.digitalchemistry.co.uk info@digitalchemistry.co.uk +44 (0)113 2181850 The Iron Shed, Harewood House Estate, Leeds, LS17 9LF, United Kingdom Contact Us

More Related