1. Instant JChem INFORMATICS MATTERS
Informatics solutions for drug discovery

2. Instant JChem is…
An “out of the box” desktop application designed for biologists and chemists
A fast and scalable database application for chemistry
A modular platform for developing future chemistry applications

3. Aims of Instant JChem
Provide a desktop alternative to current applications such as ISIS, Accord etc.
Easy to install, manage and update
Maintain an open modular extensible platform to allow new functionalities to be continually added (by users, ChemAxon and ChemAxon partners)
Integrate other ChemAxon toolkits upon demand
Client led development
Fully documented and supported
Localizable

4. Key strengths Ease of deployment in multi user environment
Flexible deployment options
Simple and easy to use
Fast and scalable
Easy to create form and table based reports
Powerful search functionality
Powerful chemistry functionality
Import, export and merge capabilities
Modular and extensible

5. Database creation Create databases in seconds
Multiple databases can be open
Local and remote databases supported
Derby, Oracle, MySQL
Customize by defining additional fields
Support for relational data
Support for multiple structure table types
Molecule, Reaction, Query, Markush, Any Structures
For more information about database handling and search:

6. Import and export
Flexible options for defining how to import files into the database
Merge data from multiple files into one dataset
Export wizard allows data to be exported to files
Standard file formats supported such as SD & RD files and Daylight smiles
Support for multiple encodings (e.g. Japanese text)

7. Calculations and predictions
Add calculated or predicted properties using chemical terms fields
Values automatically updated when structures edited or added
Wide range of functions available
Examples:
logP/logD
pKa
H-bond donor/acceptors
Lipinski rule of 5
Bioavailability
IUPAC Name
Can be used as filters for searches
For more information about structure based prediction and other functions of ChemAxon’s Chemical Terms:

8. Chemical business rules - Standardizer
Control the way structures are handled
Nitro group representation
Counter-ions
Explicit hydrogen atoms
Tautomers
For more information about structure canonicalization:

9. Grid View A chemically aware table suitable for very large data sets
Multiple views can be open and visible at any one time
Data in the table can be sorted, queried and formatted
Structure changes update predicted properties dynamically
Various display options are possible

10. Form view Custom forms can be designed.
Relational data can be displayed
“Snap to edges” aids form design
Form Widgets are bound to data fields
Form widgets expected to become major extension point
Extensible widgets and renderers

11. Flexible display options
Views can be configured to format data according to users needs
Here options for structure display are being specified
Support for 2D and 3D structure display
Support for sub-structure highlighting and alignment to query structure

12. Relational data
Relational data can be displayed in master-detail forms
Relational models can be built using the Schema and Data Tree editors
“Relationships” modelled on (and use) database foreign key constraints
Import of relational data from MDL’s RDF format files.

13. Query
Form based query and query builder provide alternative ways of defining queries
Complex queries are rapidly executed even with millions of structures
Indexes can be added to improve performance
Relational and AND and OR type queries can be specified
Filter results with chemical terms expressions
Alignment and substructure highlighting in results
For more information on search features:

14. Query extensions Overlap analysis Federated search
Compare one set of structures with another
Federated search
Run a structure search across multiple structure tables at once

15. List and Query Management
Queries can saved and re-executed
Lists of results can be saved and restored
Queries can be restricted to a list of entries
List and queries can be copied or shared between users
Lists can be combined with Intersection, Union, XOR, A not B logic

16. Markush search and enumeration
Markush table type for storing Markush structures
Combinatorial libraries
Patents
Perform structure searches against the Markush structures
Enumerate a Markush structure
Full enumeration
Random enumeration
Enumerate within context of a query structure

17. Deployment 1. Traditional installer 2. Java Web Start
Updated modules can be downloaded and installed
Allows you to keep up to date with the latest features and fixes
Customers can configure their own update center
Distribute your own plugins
2. Java Web Start
Zero install option
Deployable at customer’s site

18. Multi-user environments
Pre-configured settings for multi-user environments
Centralised deployment through Java Web Start
Centralised project and connection configuration
Centralised license management
Multi-user databases
Access control
Sharing of views, queries, lists
‘IJC URLs’: click on a hyperlink in web/ and:
IJC opens (installing if necessary)
Open the specified view
Apply the specified query or list

19. Licensing ‘Personal’ (no license required)
Free for commercial and academic users
Local databases only - no search limitations
Default standardization included (custom standardization requires standardizer license)
Most chemical terms functions require calculator plug-in licenses
Markush features need licenses
‘Enterprise’ (requires license)
Shared databases (Oracle and MySQL)
Multi-user collaboration
‘Calculations pack’ (requires license)
All calculator plugins
Standardizer
Only for use in a local database

20. IJC Development curve Rapid development since Jan 2006 start
IJC 1.0 Nov 2006
IJC 2.0 Aug 2007
IJC 2.1 Sep 2007
IJC 2.2 Jan 2008
IJC 2.3
Apr 2008
Database creation
Local and remote DBs
File import/export
Query
Spreadsheet view
Overlap analysis
Form view
Relational data
Advanced query
Multi user access
Security
API
List management
Query management
Form based query
Shared views, lists, queries
Federated search
LDAP based security
Export to Excel
Java Web Start
Form printing
Marvin/JChem 5.0
Shared projects
IJC URLs
Markush features

21. Future developments Development is rapid and accelerating
capacity is being doubled (2007 Q1 vs 2008 Q1)
User feedback drives future development
Functionality
Architecture
ChemAxon tools
Applications
More field types (esp. biological types)
More display widgets
Calculated fields
Charting & visualisation
Conditional formatting
IJC server
Improved API
Scripting
Pivoted data
JChem cartridge
Reactor
LibMCS
JKlustor
Marvin Space
R-group analysis
New licensing system
Chemical Registration
Assay data management
Virtual screening
Library design

22. Further information Web pages & Download Licensing Support forum
Licensing
Support forum
Animations