Java Solutions for Cheminformatics Feb 2008 What’s new for PP
Mar 26, 2015
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