Instant JChem is a desktop application for end user scientists. With Instant JChem you can create, explore and share chemical and non chemical data in local and remote databases without additional administration. Instant JChem has a wide and growing range of functionality including customizable database views, integration of library enumeration and dynamic population of columns with singular and combined molecular property and descriptor predictions.
Ease of database management on your desktop
Easy local and remote database management
In Instant JChem local and remote databases can easily be created and administered by end users. Using either a local database engine or a remote enterprise database (Oracle & MySQL) millions of structures can be explored and managed. Instant JChem allows you to open and manage several databases simultaneously. In addition to simple chemical structures you can also store non-chemical data, reactions or even Markush structures in a database. Handling relational data is supported, making Instant JChem a great tool for managing and reporting your assay and chemical data.
Flexible import and export to databases
Structure and non-structure data fields can be imported into and exported from databases using the wizard. Fields to be imported can also be selected and mapped. Apart from the standard chemical file formats (SDF, RDF, SMILES, SMARTS, CDX, SKC, InChI, etc) Instant JChem also supports Markush DARC file format.
Instant JChem as a viewer
Even without a license Instant JChem can be used to visualize data in Instant JChem projects and provides full structure search and form design capabilties, but is limited to handling data sets that are already present within the Instant JChem local database. This provides a great way to distribute data to your colleagues.
Visualization of database content
Customised grid view for database content visualisation
The grid view provides a simple means to view tabular data (or spreadsheet like). When you import data, a corresponding grid view is automatically generated for you. The grid view offers a representation of the data in the table, enabling you to both view and edit the data. Because the view is synchronized with the database table, any edits you make will cause the database table to automatically update.
Customised form view for database content visualisation
The form view allows the creation of more complex reports from relational datatables. The form builder allows multiple reports to be easily designed and laid out. You can add display widgets to the form, and bind them to particular field(s). Each widget can be re-sized and re-positioned, allowing your fine grain control of the design. Relational data can be displayed, with the contents of the widgets updating reflect the current content and selection. Forms can also be shared and copied. Furthermore, with the help of the Button Widget, which is a new feature of version 5.8, one can perform custom made actions, defined by the user in the groovy sript.
Fast and powerful structure searches on your desktop
You can search for structures by a query structure and specified search options. Similarity, substructure, full fragment, fragment, superstructure and duplicate searches are directly available in Instant JChem. It is possible to apply further structure filtering sequentially to narrow the hit list. Structure searches can be combined with other datafield searches via ChemAxon’s Chemical Terms language. An overlap analysis function lets users compare the entire contents of two database tables using any of the structure search operators. Federated searches enables users to perform structure searches on several datatables simultaneously.
List and query management
Instant JChem contains powerful list and query management features, allowing queries and hit lists to be saved and re-used at a later time. Lists can be combined using logical (AND, OR, NOT…) operators, and lists for different fields can be managed and inter-converted.
Standardizer is a structure canonicalization tool for converting molecules from different sources into standard representational forms and could be considered as allowing building of chemical business rules. Standardizer can automate the identification of mesomers, tautomers, stereoisomers and counter-ion removal. Aromatization or cleaning can also be automatically applied. Using the Standardizer wizard within Instant JChem helps users to store the structures in a canonicalized form that is essential for accurate structure searches.
Facilitating Medicinal Chemistry on your desktop
Synthetically feasible virtual library generation
Instant JChem uses ChemAxon’s Reactor, a synthesis engine for virtual library generation. The reaction can be chosen from ChemAxon’s ‘smart’ reaction library, or entered by the user. The reactants are sourced from IJC database table(s), and products are written into a new database table. Reagents can be arranged in a sequential or combinatorial mode. Products or the whole reaction can be generated.
ChemAxon’s empirical smart rules are available in Instant JChem, predicting the reactivity and selectivity and can be specified by the user through a generic reaction. For more about generating generic reaction see Reactor rules.
ChemAxon’s enumeration technology allows applying empirical ‘smart’ rules in Instant JChem, predicting the reactivity and selectivity. Reactivity rules are boolean expressions describing natural conditions – these conditions should be satisfied, otherwise the reaction does not take place. Selectivity rules are real-valued chemical expressions that order products according to their occurrence. Through applying and tuning these rules the user can define libraries that are synthetically feasible.
Competitor analysis is one of the major steps during drug discovery. Researchers can investigate a smaller set of patent IUPAC names which can be imported directly and will automatically be converted into structures, then further characterized. IUPAC names can also be generated for existing datasets which can be used in the patent application.
Fast 2D/3D cleaning
Often imported chemical structures do not look correct. Users can clean structures easily either in 2D or 3D using the built-in Standardizer module. The calculation generates acceptable 3D structures and conformers of a given molecule. The 3D structure (conformation) strongly affects the properties and the reactions of molecules, so a medicinal chemist can have a first quick estimation in Instant JChem about the 3D representation which often has an intuitive value during research.
Physical-chemical property and molecular descriptor calculations
A key feature Instant JChem is the degree of integration of our structure based calculations (Calculator Plugins). Directly from Instant JChem users can populate columns with physico-chemical properties, molecular descriptors and topology analysis results. Various indices used in drug discovery are also implemented such as Lipinski drug-likeness. Chemical Terms, a language for combining and extending Calculator Plugins is also natively integrated, letting users easily set up complex structure based arguments to populate cells. Another benefit of the deep integration is that adding new rows or editing structures automatically updated dependent columns.
Instant JChem supports advanced graphical visualization of database content using various chart formats. The charts are fully synchronised with the query and selection features, allowing interactive browsing and visualisation of data.
Analyze your data in a Histogram or Scatter plot
New widgets can be used in the form designer to plot data points in an interactive way facilitating visual analysis of chemical structures and related datasets. Calculated or standard fields can be displayed and data points or bars can be selected and propagated to other widgets so that user directly can identify the data points belonging to a particular chemical structure.
Wide selection of widgets and formatting options
Tabbed pane widgets allow users increase complexity of a form when there are different fields, e.g. Molecular properties and Assay data, belonging to a chemical structure and creating separate boxes would be confusing.
Multi-field sheet widget further offers way to create a two column table with the first column being the field names and the second being the value for the field for the current row. This provides a more compact way to display data than the current range of widgets allow, and allow fields to be grouped together into sets.
Chemical structures can also be visualized in a dense matrix representation similarly to the current table widget, but with one structure per cell rather than one per row. An additional data field can also be displayed so that you can display the compound ID alongside each structure.
Users have the ability to format data and colour the background of cells in tables or widgets in form based on criteria specified by the user using the conditional formation improvement.
Powerful data visualization and statistical analysis
The integration of Instant JChem with TIBCO’s Spotfire Professional results in a powerful tool allowing researchers to speed up the analysis of large chemical libraries. Instant JChem’s key new feature, the personal server, plays a important role in setting up this connection.
It can be started from IJC directly, and as an active interface using OData open communication protocol it manages the data transfer between the clients. This interactive process makes sharing structural and non-structural information with Spotfire seamless. Once loaded into Spotfire, the data can be processed with powerful analytical and visualization methods producing results for high quality reports.