standardizer molecular cosmetics for chemoinformatics györgy pirok nóra máte istván cseh...
TRANSCRIPT
Standardizer
Molecular Cosmetics for Chemoinformatics
György PirokNóra MáteIstván CsehSzilárd DórántPéter KovácsSzabolcs CsepregiFerenc Csizmadia
Why standardize structures?
Canonicalisation Uniformization of structures without changing the chemical content to
recognize duplicates, functional groups (aromatization, mesomers, tautomers, ... )
Beautification Making the structures visually more attractive (dearomatization,
cleaning coordinates, wedge orientation, ... )
Modification Conversion of structures by modifying its original content as a
preparation step for further chemoinformatics tasks (transformations, removing stereo, removing R-groups, ...).
often difficult to categorize the standardization actions
Canonicalisation
making hydrogens explicit
converting to canonical mesomer form
transforming to user defined mesomer form
Hydrogens
aromatizing Kekülé rings
Resonant structures
converting to canonical tautomer form
removing user defined fragments
transforming to user defined tautomer form
Tautomers
expanding stoichiometry
Other
removing small fragments
making hydrogens implicit
setting the chiralflag
Mesomers
Tautomersoxo-enol, enamine-imine
Tautomerspyridone-pyridol
Fragment removal
Specific counterion removal
Solvent removal
Stoichiometry expansionexpanding salt stoichiometry
Stoichiometry expansionexpanding reaction stoichiometry
Beautification
calculating 2D coordinates
Hydrogens
converting aromaticrings to Kekülé format
Resonant structures
making hydrogens implicit
Cleaning
reallocating wedge bonds
contracting/expanding/ungrouping abbreviated and multiple groups
Groups
template based cleaning
3D geometry optimization
Template-based Cleaning2D-coordinate calculation of macrocycles or bridged systems
query
Template-based Cleaningaligning search results to the query
client
Canonicalization During Database Import
RelationalDatabase
input structures
canonicalization configuration original structurescanonicalized structures
server
StandardizerJChem Base/ Cartridge
client
Sending Query to the Database
RelationalDatabase
serverquery structure
canonicalization configuration canonicalized queryquery is compared
to the canonicalized structures
StandardizerJChem Base/ Cartridge
Displaying Result Structures
RelationalDatabase
original structures
serverclient
beautification configuration
beautified structures
StandardizerJChem Base/ Cartridge
Modification
custom transformations+
API and command line interface
Standardizer st = new Standardizer(new File("standardize.xml"));st.standardize(mol);
standardize input.sdf -c config.xml -o output.smiles
Live Demonstration
Applications: Virtual Synthesis
Applications: Structure Databases
How can ChemAxon Help
Free for non commercial websites
Free for academic teaching and research“Academic Package”
Free Academic Package to be extended to cover academic networks – campus-wide roll out
Acknowledments
Ferenc Csizmadia Nóra Máté István Cseh Szabó Attila Szilárd Dóránt Péter Kovács Szabolcs Csepregi