JChem Base

chemical interface to relational database engines

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Version 5.12.4
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Search Engine Presentation
Structure Search Overview
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JChem Base is a tool for the development of cheminformatics applications allowing storage and search of structural and non-structural data. JChem Base can handle molecule, reaction, polymer, Markush and query structural contents. JChem Base will integrate with a variety of database systems (Oracle, MS SQL Server, DB2, Access, etc) with web interfaces and offers fast substructure, similarity, exact, superstructure and other searches.

General overview

Structures are stored in database tables, combining structural and non-structural data. SDF, SMILES, MOL, RDF, CML, and many other file formats are supported. JChem Base also supports ChemAxon’s Chemical Terms language to enable complex chemical queries, expressions and rules.

The system includes Marvin, a suite of chemical editor, viewer and visualization tools and graphical user interfaces.

Markush Search add-on allows the registration of generic structures into the database and substructure, full structure and duplicate searching in enumerated libraries without enumeration of library members. Learn more about Markush Search add-on »

Base features

  • Sophisticated and efficient search algorithm
  • Automatically calculated Chemical Terms columns
  • Standardizer integration
  • Ready-to-use example web applications using Marvin Applets are included in the distribution

JChem manager GUI

Advanced features

  • full structure, substructure, superstructure and duplicate matching
  • variable similarity searching including reaction similarity
  • registration and searching of polymers, mixtures and formulations
  • generic query atoms
  • various query properties supported
  • full SMARTS support including recursive SMARTS
  • R-group query expressions
  • reaction queries, including reaction mapping, reaction query features
  • stereo specific structure and reaction specifications
  • structure canonicalization
  • chemical terms support
  • different types of tautomer search
  • extensive search options

Articles in the library

Compound Progression Workflow Process Presentation

Compound progression workflow process is a mechanism to track stage, status and actions of compounds within a project to streamline drug discovery operations. This is accomplished by prov…
September 2012 Author: ()

JChem Base & Cartridge III: Structure searching in memory and visualizing re… Webinar

Continuing our previous webinar on database tasks, in this training we will give an overview about structure search in memory and visualization options. Searches can be performed without …
March 2013 Author: ()

Future-proofing Cheminformatics Platforms Publication

April 2012 Authors: , , (, , )
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Related forum threads

No license file found. Product name: Structure Search Licens (May 21st, 01:28pm)

“ Szilard wrote: Hi,   - Could you please let us know the exact JChem version in use (dispalyed in the "About" dialog) - Please send us the license file in use to support _at_ chemax...”

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Create domain index error "index already created" (May 21st, 12:40pm)

“ORA-20105: Illegal option: structureType There are two spaces between "option:" and "structureType". The first one is hard-coded to keep a space before the parameter name. The second space comes ...”

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Frequently Asked Questions

What is JChem Base?
JChem Base is a tool for the development of cheminformatic applications allowing storage and search of structural and non-structural data.
Why is JChem Base useful?
JChem Base handles molecule, reaction, combinatorial Markush and query structural contents. JChem Base integrates with a variety of database systems (Oracle, MS SQL Server, DB2, Access, etc.) with web interfaces and offers fast substructure, similarity, exact, superstructure and other searches. It is also a building block for other ChemAxon products that handle chemical structures in databases: JChem Cartridge, Instant JChem and JChem for Excel.
Who uses JChem Base?
Chemists, cheminformaticians or anyone who wants to store and search chemical structures and related data in a database.
Do I have to do programming to use JChem Base?
Not necessarily. Instant JChem, JSP, and AJAX are ready-to-use desktop applications. For customization, you may have to do programming.
What kind of additional software is needed?
Java Virtual Machine version 5 or later and a relational database engine (RDBMS) that will store the structures.

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