Standardizer

Molecular Cosmetics for Chemoinformatics

György Pirok

Java Solutions for Cheminformatics

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, ...).

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

Fragment removal

Specific counterion removal

Solvent removal

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 Cleaningorienting 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

Standardizer GUI

Applications: Virtual Synthesis

Applications: Structure Databases

Acknowledments

Ferenc Csizmadia Nóra Máté István Cseh Szabó Attila Alex Allardyce Szilárd Dóránt Péter Kovács Szabolcs Csepregi

Java Solutions for Cheminformatics