version 5.3, february 2010 scientific & technical presentation jchem base
TRANSCRIPT
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version 5.3, February 2010
Scientific & technical presentation
JChem Base
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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
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Structural overview
Web
browser
Application Web application
JChem Base API:Chemical logicStructure cache
JDBC driver: Standard interface to the RDBMS
RDBMS (e.g. Oracle, MySQL, etc.) :
Storage and security
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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.
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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
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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
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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.
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JChem Base 5.2.2, Intel Quad Q6600 2.4GHz, 8 GB RAM; Oracle 10.2.0.3
Performance (1)
Number of compounds
Elapsed time
Duplicates not checked
Duplicates 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 in PubChem (19.5 million compounds):
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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
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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
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Administration with JChemManager
User interface for• creating tables
• import
• export
• deleting rows
• dropping tables
Most functions are also available from command line.
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Standardization
• 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)
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Custom Standardization Example
afterbefore
Standardizer http://www.chemaxon.com/conf/Standardizer.ppt
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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.
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Table types
Control allowed chemical structures and available operations
• Molecule
• Reaction
• Markush
• Query
• Any structure
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The structure of JChem tables
Column name Explanation
cd_id unique numeric identifier in the table
cd_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 structure
cd_sortable_formula formula representation for alphanumerical sorting
cd_molweight the molecular weight of the standardized structure
cd_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
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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
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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)
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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
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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
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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
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Visit other technical presentations
MarvinSketch/View http://www.chemaxon.com/MarvinSketch_View.ppt
MarvinSpace http://www.chemaxon.com/MarvinSpace.ppt
Calculator Plugins http://www.chemaxon.com/Calculator_Plugins.ppt
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
JKlustor http://www.chemaxon.com/JKlustor.ppt
Fragmenter http://www.chemaxon.com/Fragmenter.ppt
Reactor http://www.chemaxon.com/Reactor.ppt