Pipelining ChemAxon Szilard Dorant Solutions for Cheminformatics

The Component Collection: Quick facts Provides access to ChemAxon tools from Pipeline Pilot Free of charge Open source : Java sources are also included Available from ChemAxon or Accelrys Latest version : 1.4 Released in November 2008 Requires JChem / Marvin 5.0.1 or better Tested against Pipeline Pilot 6.1.1

Provides access to ChemAxon tools from Pipeline Pilot

Free of charge

Open source : Java sources are also included

Available from ChemAxon or Accelrys

Latest version : 1.4

Released in November 2008

Requires JChem / Marvin 5.0.1 or better

Tested against Pipeline Pilot 6.1.1

What’s new in 2008* Direct support and development from ChemAxon 3 major releases – one about every 4 months 6 early access releases 12 new user components Several components significantly upgraded *As of November 2008 November 24 1.4 October 22 1.3.1 July 11 1.3 March 5 1.2 Date Version User interest Development

Direct support and development from ChemAxon

3 major releases – one about every 4 months

6 early access releases

12 new user components

Several components significantly upgraded

Available functionality Standardizer: structure canonicalization Chemical Terms expressions for filtering and calculations (including logP, logD, pKa, HBD, HBA, Isoelectric point, PSA and more) Reactor : “smart” virtual reaction processing Maximum Common Substructure (MCS) based clustering IUPAC Name <-> Molecule conversion (both directions) JChem chemical database: insertion, search and retrieval of structures; create and drop structure tables Marvin applets: structure visualization and editing Major microspecies (major protonation form) Microspecies distribution Burden eigenvalue descriptor (BCUT)

Standardizer: structure canonicalization

Chemical Terms expressions for filtering and calculations (including logP, logD, pKa, HBD, HBA, Isoelectric point, PSA and more)

Reactor : “smart” virtual reaction processing

Maximum Common Substructure (MCS) based clustering

IUPAC Name <-> Molecule conversion (both directions)

JChem chemical database: insertion, search and retrieval of structures; create and drop structure tables

Marvin applets: structure visualization and editing

Major microspecies (major protonation form)

Microspecies distribution

Burden eigenvalue descriptor (BCUT)

Chemical Terms Calculator Use arbitrary Chemical Terms expressions Results stored to arbitrary properties A wide range of ChemAxon functionality can be accessed as Chemical Terms functions New in 1.3

Use arbitrary Chemical Terms expressions

Results stored to arbitrary properties

A wide range of ChemAxon functionality can be accessed as Chemical Terms functions

Canonicalization with Standardizer Simple to use, but now full complexity is also available: Simple actions (checkboxes) Configuration string (simple or XML) Configuration file Upgraded in 1.2

Simple actions (checkboxes)

Configuration string (simple or XML)

Configuration file

IUPAC naming components IUPAC Name to Molecule Molecule to IUPAC Name Example “roundtrip” protocol: New in 1.4

IUPAC Name to Molecule

Molecule to IUPAC Name

Example “roundtrip” protocol:

Reactor Improvements: Upgraded in 1.4 Synthesis code generation Output reaction mapping Advanced options: Unambiguous only Ignore rules: Reactivity and Exclude Selectivity Tolerance

Synthesis code generation

Output reaction mapping

Advanced options:

Unambiguous only

Ignore rules:

Reactivity and Exclude

Selectivity

Tolerance

Combinatorial Reactor Example

Clustering with LibMCS Maximum Common Substructure (MCS) based clustering Size of smallest common substructure to consider Three levels of heuristics: Exact (no heuristics) Fast Very Fast Bond type, atom type, charge can optionally be ignored Disallow “breaking” rings (default) Options: New in 1.4

Size of smallest common substructure to consider

Three levels of heuristics:

Exact (no heuristics)

Fast

Very Fast

Bond type, atom type, charge can optionally be ignored

Disallow “breaking” rings (default)

JChem Base Insert Returns cd_id (primary key) values Two input modes: read structure source from a specified property if property not specified uses PP input molecule Insert into additional data fields* New features: *Under development, currently limited to string database column types Duplicate filtering option (using Pass and Fail ports) Upgraded in 1.2

Returns cd_id (primary key) values

Two input modes:

read structure source from a specified property

if property not specified uses PP input molecule

Insert into additional data fields*

Duplicate filtering option (using Pass and Fail ports)

JChem Database Search Several search options were added Easier protocol integration and better performance due to concentrated functionality Upgraded in 1.2

Several search options were added

Easier protocol integration and better performance due to concentrated functionality

JChem Base demo protocol

Improved error reporting Helps to track down problems quicker More information is displayed in the error dialog: Marvin or JChem version, the current structure, etc. Utility component for displaying ChemAxon environment (from 1.4) If the environment variable CHEMAXON_PP_LOG_DIR is set, an even more detailed error report will be appended to the file &quot;pp_error.txt&quot; in the specified directory New in 1.3

Helps to track down problems quicker

More information is displayed in the error dialog: Marvin or JChem version, the current structure, etc.

Utility component for displaying ChemAxon environment (from 1.4)

If the environment variable CHEMAXON_PP_LOG_DIR is set, an even more detailed error report will be appended to the file &quot;pp_error.txt&quot; in the specified directory

Planned components JChem Cartridge for Oracle Integration with Instant JChem Tautomer generation Conformer generation Conversion of various structure file formats Node release cycle is fast and flexible. Please advise us on priority and additional functionality for future node development.

JChem Cartridge for Oracle

Integration with Instant JChem

Tautomer generation

Conformer generation

Conversion of various structure file formats

Node release cycle is fast and flexible. Please advise us on priority and additional functionality for future node development.

Resources Download: http://www.chemaxon.com/integration/download.html http://accelrys.org/pipelinepilot/chemistry.html Technical support forum: http://www.chemaxon.com/forum/forum88.html E-mail: Dorant__at__chemaxon_._com

Download:

http://www.chemaxon.com/integration/download.html

http://accelrys.org/pipelinepilot/chemistry.html

Technical support forum:

http://www.chemaxon.com/forum/forum88.html

E-mail:

Dorant__at__chemaxon_._com

Acknowledgements Accelrys Moises Hassan Ton van Daelen Keith Burdick Informatics Matters Tim Dudgeon ChemAxon Gy ö rgy Pirok Mikl ós Vargyas Zsolt Moh á csi

Accelrys

Moises Hassan

Ton van Daelen

Keith Burdick

Informatics Matters

Tim Dudgeon

ChemAxon

Gy ö rgy Pirok

Mikl ós Vargyas

Zsolt Moh á csi