version 5.3, February 2010

Scientific & technical presentation

JChem Base

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

web-based or standalone applications

in association with other ChemAxon tools

Structural overview

Web

browserApplication Web application

JChem Base API:Chemical logicStructure cache

JDBC driver: Standard interface to the RDBMS

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

Storage and security

Compatibility and integration

File formats:• SMILES• MDL molfile (v2000 and v3000)

• MDL SDF• RXN• RDF• MRV• IUPAC name, InChI• Markush DARC• CDX

Integration:extensive API for• Java• .NET• JChem Cartridge for Oracle

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

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

See detailed information on structure search: www.chemaxon.com/conf/Structural_Search.ppt

• 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

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•etc.

JChem Base 5.2.2, Intel Quad Q6600 2.4GHz, 8 GB RAM;Oracle 10.2.0.3

Performance (1)

Number of compounds

Elapsed timeDuplicates not

checkedDuplicates checked

10,000 21 s 26 s

100,000 2 min 4 s 2 min 34 s

200,000 4 min 24 s 5 min 13 s

Query Number of hits Search time

2 0.91 s

93 0.98 s

6,001 1.30 s

146,256 5,66 s

Compound registration:

Substructure search inPubChem (19.5 millioncompounds):

Performance (2)

Similarity search:Tanimoto >0.9

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

Query Number of hits Search time

0 3.39 s

0 3.82 s

0 3.33 s

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

User interface for• creating tables• import• export• deleting rows• dropping tables

Most functions are also available from command line.

Standardization

• Default standardization includes:

– Hydrogen removal

– Aromatization

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

Custom Standardization Example

afterbefore

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

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

Control allowed chemical structures and available operations

• Molecule

• Reaction

• Markush

• Query

• Any structure

The structure of JChem tables

Column name Explanationcd_id unique numeric identifier in the tablecd_structure the imported structure in the original format, without

modifications (except for the removal of data fields)cd_smiles; cd_smarts; cd_markush

the standardized structure format dependig on the different table types, used by the search process

cd_formula the formula of the standardized structurecd_sortable_formula formula representation for alphanumerical sortingcd_molweight the molecular weight of the standardized structurecd_hash; cd_flags;cd_fp…

fields used internally for structure searching

cd_timestamp the date and time of the insertion of the row[user fields] custom data fields can be added by the user

Structural search in database

Two stage method provides optimal performance:

1. 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)

2. Graph search algorithm is used to determine the final hit list

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

• 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

Summary

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

Links

• JChem home page:http://www.chemaxon.com/products/jchem-base

• Online tryout:http://www.chemaxon.com/jchem/examples.html

• API documentation:http://www.chemaxon.com/jchem/doc/api/index.html

• Brochure:www.chemaxon.com/brochures/JChemBase.pdf

Visit other technical presentations

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JChem Base http://www.chemaxon.com/JChem_Base.ppt

JChem Cartridge http://www.chemaxon.com/JChem_Cartridge.ppt

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

Screen http://www.chemaxon.com/Screen.ppt

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Fragmenter http://www.chemaxon.com/Fragmenter.ppt

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