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Scientific & technical presentation JChem Base. version 5.3, February 20 10. Introduction to JChem Base . High performance Java based tools for: storage , search and retrieval of chemical structures and associated data The components can be integrated into

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Version 5 3 february 2010

Scientific & technical presentation

JChem Base

version 5.3, February 2010

Introduction to jchem base

Introduction to JChem Base

High performance Java based tools for:

storage, search and retrieval of chemicalstructures and associated data

The components can be integrated into

web-based or standalone applications

in association with other ChemAxon tools

Version 5 3 february 2010

Structural overview



Web application


JChem Base API:

Chemical logic

Structure cache

JDBC driver: Standard interface to the RDBMS

RDBMS (e.g. Oracle, MySQL, etc.) :

Storage and security

Compatibility and integration

Compatibility and integration

File formats:


  • MDL molfile (v2000 and v3000)


  • RXN

  • RDF

  • MRV

  • IUPAC name, InChI

  • Markush DARC

  • CDX


  • extensive API for

  • Java

  • .NET

  • JChem Cartridge forOracle

Database engines:

  • Oracle

  • MySQL

  • MS SQL Server

  • PostgreSQL

  • MS Access

  • IBM DB2

  • Derby

  • etc.

    Operating systems:

  • Windows

  • Linux

  • Mac OS X

  • Solaris

  • etc.

Jsp example application

JSP example application

  • Features:

    • Substructure, Superstructure, Full, Exact fragment, Similarity and Perfect search

    • Molecular Descriptor similarity search with descriptor coloring

    • Substructure hit alignment and coloring, inverse hit list

    • Chemical Terms filter

    • Import / Export

    • Export of hits

    • Insert / Modify / Delete structures

    • AJAX in JChem Webservices

Structure search features

Structure search features

  • Wide range of query atoms

  • Query properties

  • R-group queries

  • Full SMARTS support

  • Coordination compounds

  • Link nodes

  • Pseudo atoms, lone pairs

  • Relative stereo

  • Reaction search features

  • Hit coloring, position variation

  • Polymers

See detailed information on structure search:

S earch options

Search options

Some selected structure search options:

Stereo on/off

Ignore charge/isotope/radical/valence/polymers, etc.

Vague bond matching options

Chemical Terms filter

Tautomer search

Inverse hit list

Maximum search time / number of hits

Combine with non-structure conditions

Ordering of results


Performance 1

Performance (1)

Compound registration:

Substructure searchin PubChem(19.5 million compounds):

JChem Base 5.2.2, Intel Quad Q6600 2.4GHz, 8 GB RAM;


Performance 2

Performance (2)

Similarity search:Tanimoto >0.9

JChem Base 5.2.2, Intel Quad Q6600 2.4GHz, 8 GB RAM;Oracle 10.2.0.

Markush structures

Markush structures

  • Markush structure registration and search

  • Markush features

    • R-groups

    • Atom lists, bond lists

    • Position variation bond

    • Link nodes and repeating units

    • Homology variation (alkyl, aryl, etc.)

  • Compatible Markush enumeration plugin

Administration with jchemmanager

Administration with JChemManager

User interface for

  • creating tables

  • import

  • export

  • deleting rows

  • dropping tables

    Most functions are also available from commandline.



  • Default standardization includes:

    • Hydrogen removal

    • Aromatization

  • Custom standardization can be specified for each table by specifying an XML configuration file at table creation or in the “Table Options” dialog of JChem Manager (jcman)

Custom standardization example




Custom Standardization Example

The property table

The property table

The property table stores information about JChem structure tables, including:

  • Fingerprint parameters

  • Custom standardization rules

  • Other table options and information

    More than one property table can be used, each property table represents a particular JChem environment.

Table types

Table types

Control allowed chemical structures and available operations

  • Molecule

  • Reaction

  • Markush

  • Query

  • Any structure

The structure of jchem tables

The structure of JChem tables

Structural search in database

Structural search in database

Two stage method provides optimal performance:

  • Rapid pre-screening reduces the number ofpossible hit candidates

    • Chemical Hashed Fingerprints are used forsubstructure and superstructure searches

    • Hash code is used for duplicate filtering(usually during compound registration)

  • Graph search algorithm is used to determine the final hit list

Structure cache

Structure Cache

  • Contains Fingerprints for screening and ChemAxon Extended SMILES for ABAS

  • Instant access to the structures for the search process

  • Reduced load on the database server

  • Incremental update ensures minimum overhead after changes in the table

  • Small memory footprint due to

    • SMILES compression

    • Optimized storage technique

  • Approximately 100MB memory needed for 1 million typical drug-like structures (using default, 512 bit long fingerprints)

Future plans

Future plans

  • Graphical user interface for R-group decomposition

  • Arbitrary table structure (Java and .NET API for JChem index)

  • Maximum common substructure search type

  • Additional layer: JChem Server (later also as grid)

  • Compound registration system API



ChemAxon’s JChem Base API provides sophisticated high performance tools for the developer to deal with chemical structures and associated data.

Building on the JChem API is convenient, because:

  • Our various tools integrate seamlessly

  • Both high and low level API classes are available

  • Responsive developer-to-developer support



  • JChem home page:


  • Online tryout:


  • API documentation:


  • Brochure:


Version 5 3 february 2010

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