Java Solutions for Cheminformatics

Feb 2008

What’s new for PP

CXN Toolkit and applications overview

In action: MarvinView and MarvinSketch

In action: Calculator Plug-ins

Chemical Terms

Features

• Fast and sophisticated searching(chemical and non-chemical data, Chemical Terms filter, many options)

• Custom standardization

• Calculated columns

• Combinatorial Markush structure tables

Interfaces

• Integration with most relational database engines

• JChem Cartridge for tight Oracle SQL integration

• JSP integration – open source web example

• Desktop-ready through Instant JChem

Structure management and search in JChem Base

DB2

JChem Database Search

• Several search options were added

• Easier protocol integration and better performance due to concentrated functionality

Canonicalization with Standardizer

• Aromatize/dearomatize

• Add/remove explicit hydrogens

• Convert mesomers / tautomers / functional groups

• Remove solvents counterions by list smallest fragment retain largest fragment

• Set/Remove chiral flag, remove stereo features

• Ungroup S groups

• Enumerate by stoichiometry values

• 2D, 3D coordinate generation (cleaning)

• Template based cleaning

Canonicalization with Standardizer

Simple to use, but now full complexity is also available:

• Simple actions (checkboxes)

• Configuration string (simple or XML)

• Configuration file

Virtual Synthesis with Reactor

Effective‒ focused, combinatorial and

diverse libraries‒ combinatorial, random and

exhaustive dispatching‒ high throughput

Flexible‒ memory, file and database

operations sequential or combinatorial mode

‒ compound or reaction output type‒ reverse direction

Compatible – reactions: MRV, RXN, RDF,

SMARTS/SMIRKS – compounds: MRV, MOL, SDF,

SMILES – mapping: ChemAxon, Daylight,

automapper

Smart –chemo-, regio- and stereospecific–customizable

Combinatorial Reactor Example

Instant JChem as PP file viewer

Use Pipeline Pilot to create and update databases that can be intuitively searched and analyzed using Instant JChem

• Simple connect to external databases and share your native database simultaneously

• Powerful search functionalities

• Scalable – explore ’00,000’s+ live structures

• Dynamically predict properties using Calculator Plugins

• Apply canonicalization rules for import and viewing

• Wide import & export options / Merge data sets into a single set

• Form building, analysis & Reporting

• Java Web Start and API simplify deployment enterprise wide

Current developments - node building support

• New nodes to support current ChemAxon functionality

• More compatibility with existing nodes/functionality

• Support for newer functionality more quickly

• Support for PP nodes from ChemAxon directly

ChemAxon took over responsibility for building and supporting ChemAxon toolkit Pipeline Pilot nodes from Scitegic.

Available components

– Standardizer– Chemical Terms expressions– Reactor– JChem chemical database: insertion, search and

retrieval of structures– Calculator plugins (HBA, HBD, Isoelectric point,

logP, logD, pKa, Polarizability, Refractivity , TPSA)– Marvin sketcher and viewer– Major microspecies (major protonation form)– Microspecies distribution– Burden eigenvalue descriptor (BCUT)

Planned components

– JChem Cartridge for Oracle – Instant JChem end user desktop cheminformatics

solution– Name to structure, structure to name generation – Tautomer and conformer generation – Conversion of various structure file formats – MCS based clustering

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

Under development - general

• Marvin new framework = ‘prettier’, multiple skins, more customizable for users and developers

• Markush structure handling in JChem Base / Cartridge / Marvin

• Markush enumeration Plugin

• Name to structure conversion

• Solubility Calculator Plugin

• Metabolite and Metabolic Stability Prediction

• Toxicity Prediction

• Human CP450 biotransformation library

• Multi-step reactions in Marvin and JChem

• Virtual Synthesis Module for Instant JChem

• Application for compound registration system

• QSAR based on 3D conformers

Find out more

• Product descriptions & links– www.chemaxon.com/products.html

• Forum– www.chemaxon.com/forum

• Presentations and posters– www.chemaxon.com/conf

• Download JChem/Marvin and nodes – http://www.chemaxon.com/download.html