Instant JChem INFORMATICS MATTERS Informatics solutions for drug discovery

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

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

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

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: http://www.chemaxon.com/conf/JChem_Base.ppt

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)

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: http://www.chemaxon.com/jchem/doc/user/ChemicalTerms.html

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: http://www.chemaxon.com/conf/Standardizer.ppt

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

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

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

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.

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: http://www.chemaxon.com/conf/Structural_Search.ppt

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

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

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

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

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/email and: IJC opens (installing if necessary) Open the specified view Apply the specified query or list

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

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

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

Further information Web pages & Download Licensing Support forum http://www.chemaxon.com/instantjchem Licensing sales@chemaxon.com Support forum http://www.chemaxon.com/forum/forum62.html Animations http://www.chemaxon.com/anim/ijc.html