CambridgeSoft Solutions CambridgeSoft Research Informatics Louis Culot Executive Director, Research Informatics Division
Informatics Overview ChemDraw since 1986. Comprehensive Chemoinformatics since 1998. Web-based, client/server, and toolkit approaches. Native Oracle (cartridge) and Microsoft technology. Experience in large-scale and worldwide deployments.
Application Advances Background. CS product line. Application overview. Application advances.
Application Advances Information Hubs. Compounds (Registration System). Assets (Inventory Manager). Intellectual Property (E-Notebook Enterprise). Experimental Results (BioAssay HTS). Registration Inventory E-Notebook BioAssay HTS ChemACX Merck Index Derwent, etc. Compounds Assets I.P. Experiment data
Application Advances Global Login Application Integration BioSAR Browser Registration Inventory E-Notebook BioAssay HTS ChemACX Merck Index Derwent, etc. Compounds Assets I.P. Experiment data
Application Advances ChemDraw ChemFinder/Cartridge Application APIs Global Login Application Integration BioSAR Browser Registration Inventory E-Notebook BioAssay HTS ChemACX Merck Index Derwent, etc. Compounds Assets I.P. Experiment data
Application Advances WebServer 2004 Core (all applications): Hit-list management (native Oracle): Basic list operations (union, intersect, subtract). Query management. Oracle Cartridge structure engine.
Application Advances
Application Advances Chemical Registration Row-level security. Improved SDFile export. Global login. Integration with Inventory Manager, BioAssay HTS, BioSAR.
Application Advances Inventory Reagents, Registered compounds, Plates. Tight integration with BioAssay HTS, ChemACX. Plate inventory XML plate reformatting. Maintenance of molar amounts and molar concentrations.
Application Advances Inventory (plate view)
Application Advances BioAssay HTS New Assay set up. Performance improvements (HTS). Advanced graphing. Assay templates.
Application Advances BioSAR Browser Flexible reporting. Improved performance. Improved GUI, form set up. In use with > 100 child tables. Oracle Cartridge allows for true chemical data integration.
Application Advances Oracle Cartridge Faster indexing. Support for nomenclature (CDXTONAME). Support for Linux, HP/UX, Solaris, IBM AIX, Windows. True 64-bit platform. New chemical intelligence features. Oracle 9iRAC and 10G support: Searches run in own thread space.
Application Advances BioSAR + Oracle Cartridge Use over ISIS, RS3, Daylight, dbs. [ISIS, RS3, Daylight, etc.] Replication Triggers BioSAR MolFiles, SMILES, CDX 1 MolFile 2 MolFile 3 MolFile 4 MolFile MolFile 1 MolFile 2 MolFile 3 MolFile 4 MolFile MolFile DB DB Source Source DB Source DB Source CS Cartridge
Application Advances E-Notebook Web deployments at select accounts. 21 CFR 11 support. Extensive configurability. Document transition/state configuration (e.g., signatures). Data migration from 7.0.x to Web ELN. Combinatorial chemistry enumeration. Stateless middle tier / scalability investment.
Application Advances 21 CFR 11 Audit Trail
Collaborative Development R&D Customer Collaborations Registration, Row-level security, E-Notebook (7), Inventory, Plate Inventory, BioAssay HTS, BioSAR Browser, ChemFinder/Oracle, Web E- Notebook 21 CFR 11. Project security using Oracle fine-grain access control.
Stereochemistry Stereochemistry Rules: Unspecified stereochemistry (a plain bond) may match any stereochemistry (either a wedged, hashed, or a plain bond) Specific bond types need not match as long as the overall stereochemistry at a given atom does match Implicit hydrogens are taken into consideration in both the query and the target if doing so helps to determine the chirality
Stereochemistry Stereochemistry Options: Match tetrahedral stereo Match double bond stereo Thick Bonds Represent Relative Stereochemistry Absolute Relative Stereochemistry
Stereochemistry Example: HO N H O OH With Match Tetrahedral Stereo enabled, a structure search for this structure: HO N H O OH H N OH Does not find HO O Does find H N OH HO O N H OH HO O HO O HO O N H OH N H H OH
Stereochemistry Example: With Match Double Bond Stereo enabled, a structure search for this structure: OH Cl OH Cl Does not find Does find OH OH OH
Stereochemistry Example: With match Thick Bond Represent Relative Stereochemistry enabled, a structure search for this structure: HO HO HO Does not find Does find Cl Cl HO Cl Cl
Nomenclature Name=Struct Name=Struct is a technology for converting systematic and common names into their corresponding chemical structures this technology is built in for use in all of the ChemOffice suite of products For Example: (1R)-1,7,7-Trimethylbicyclo[2.2.1]heptan-2-one oxime HO N H 2 N Phosphine, tris(3-aminophenyl),oxide P O H 2 N NH 2
Nomenclature Name=Struct For Example: 2-(N-ethoxybutyrimidoyl)-5-(2-ethoxythiopropyl)-3-hydroxy-2-cyclohexen-1-one OH O N S O O N 1,2-Bis(p-dimethylaminophenyl)-1,2-ethanedione N O O
Nomenclature Struct=Name Struct=Name is a technology for converting chemical structures into their common names this technology is built in for use in all of the ChemOffice suite of products For Example: S O Cl HO OH N (R)-1-methyl-4-(prop-1-en-2-yl)cyclohex-1-ene OH S 2-hydroxybutanedicarbothioic O,O-acid diphenylcarbamic chloride H 2 N O O O bicyclo[2.2.1]heptan-2-yl formate OH O m-tolyl 4-amino-2-hydroxybenzoate
Property Prediction Common properties (2D): HNMR, 13CNMR clogp Molar Refractivity Molecular Weight H-Bond donors H-Bond Acceptors Custom screening
Toolkits Oracle Cartridge Business-tier tools Client-side tools
Toolkits Oracle Cartridge Native Oracle Cartridge developed largely in C++. Oracle 8i, 9i, 32-bit and 64-bit. HP/UX, Solaris, Windows, Linux, IBM AIX. Chemical-format neutral: Supports CDX, SMILES, MolFile. Dynamically converts between formats. Nomenclature (Struct<->Name). Option to wire property predictions.
Toolkits Business-tier tools Substructure searching. Library enumeration. Property prediction. 2D->3D conversion. Nomenclature tools (struct=name)
Toolkits Client-side tools ChemDraw ChemDraw plug-in (Netscape, Macintosh clients) ChemDraw Active-X» IE clients» VB, C++ applications Chem3D Active-X ChemFinder» ChemFinder now support native Oracle Cartridge connections. E-Notebook Active-X
Thank You!!!
CambridgeSoft Solutions CambridgeSoft Research Informatics