Instant JChem (IJC) April 2008 Confidential. Copyright© 2008 ChemAxon Kft, Informatics Matters Ltd Instant JChem INFORMATICS MATTERS Informatics solutions

Instant JChem (IJC) — April 2008Confidential . Copyright© 2008 ChemAxon Kft, Informatics Matters Ltd

Instant JChem

INFORMATICSMATTERS

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– 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• 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

IJC 1.0Nov 2006

IJC 2.0Aug 2007

IJC 2.1Sep 2007

IJC 2.2Jan 2008

IJC 2.3Apr 2008

Database creationLocal and remote DBsFile import/exportQuerySpreadsheet viewOverlap analysis

Form viewRelational dataAdvanced queryMulti user accessSecurityAPI

List managementQuery management

Form based queryShared views, lists, queriesFederated searchLDAP based securityExport to ExcelJava Web StartForm printing

Marvin/JChem 5.0Shared projectsIJC URLsMarkush features

• Rapid development since Jan 2006 start


Future developments

Functionality Architecture ChemAxon tools Applications

More field types (esp. biological types)

More display widgets

Calculated fields

Charting & visualisation

Conditional formatting

IJC serverImproved APIScriptingPivoted data

JChem cartridgeReactorLibMCSJKlustorMarvin SpaceR-group analysisNew licensing system

Chemical RegistrationAssay data managementVirtual screeningLibrary design

• Development is rapid and accelerating– capacity is being doubled (2007 Q1 vs 2008 Q1)

• User feedback drives future development


Further information

• Web pages & Download

• http://www.chemaxon.com/instantjchem

• Licensing

• [email protected]

• Support forum

• http://www.chemaxon.com/forum/forum62.html

• Animations

• http://www.chemaxon.com/anim/ijc.html

Documents

Instant JChem (IJC) April 2008 Confidential. Copyright© 2008 ChemAxon Kft, Informatics Matters Ltd Instant JChem INFORMATICS MATTERS Informatics solutions