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Modern Enterprise and Standalone
Cheminformatics Solutions
Wei Deng (David)
Bio-IT World Asia
IT Infrastructure and the Cloud
June 6th, 2012
Singapore
ChemAxon Fingerprint
• Head Office in Budapest, Hungary
• Cheminformatics software – since ‘98
• Pharma, biotech, agrochem, academia
• Global sales – US, Europe, Japan, RoW
• Database management tools, drug design and
discovery, structure analysis
• >30 implementation partners, global agents,
consultancy, training
Customer Case Studies
A top global pharma company – Global Platform – Rollout of JChem for Excel implemented, Instant JChem in progress
– Full replacement of ISIS Base and Daylight
A top Japanese pharma company – Japan and US Site licenses Platform
– Full replacement of ISIS Base and ISIS for Excel in process
– Replacement of Daylight
A top U.S. pharma company – Global Platform
– Rollout of Cartridge, Instant JChem
– Full replacement of ISIS Base and Daylight
A top European pharma company – Cartridge, JChem for Excel, SharePoint, IJC
– Replacement of Accord for Excel, ISIS Base and Daylight
JChem for Excel
• Add Chemistry to Microsoft
Excel
– Structure sketching, search,
enumeration, analysis
• Combine with Excel’s
powerful features:
Functions, Sorting, Filtering,
Charts…
• Implemented in C# .NET,
and Visual Studio
– Proof that ChemAxon
APIs can be used in a
Java-less .NET
environment
• Easy to install and deploy
Instant JChem
Desktop application for local and remote chemical database
management, search and structure based prediction
Simply connect to external
databases and share your native
database simultaneously
Powerful search functionalities
Scalable – explore large datasets
(>> millions of compounds)
Dynamically predict properties
using Calculator Plugins
Apply canonicalization rules for
import and viewing
Wide import / export options
Merge data sets into a single set
Instant JChem: http://www.chemaxon.com/conf/Instant_JChem.ppt
Virtual Library Enumeration with Reactor
₪ Reaction Engine
Converts reactants according
to a given reaction scheme
Reaction mapping; chemo-,
regio- and stereospecific
reactions supported
₪ Reactor Application
An application of virtual library
enumeration based on reaction
schemes
Wizard-like application
and reaction editor.
Implemented directly into
JChem for Excel and Instant
JChem
Virtual Library Enumeration with Markush Structures
Functionality: Full
Sequential
Random
Calculate library size
Scaffold alignment
and coloring
Homology group enumeration
Post filter
Export enumerated structures
Search the Full Patent Markush Database
• Complete patent
database from Thomson
Reuters (Markush +
exemplified + non-
structural information,
dated back to 1987)
• Data internally hosted or
on Amazon Cloud
• Powerful virtual machine,
secure connection and
confidential search
• Constantly improving
search performance
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Calculator Plugins
Calculator Plugins http://www.chemaxon.com/Calculator_Plugins.ppt
Elemental Analysis
IUPAC/Traditional to Name
Protonation pKa, Major Microspecies, Isoelectric Point
Partitioning
logP, logD
Charge
Charge, Polarizability, Orbital Electronegativity
Spectrum prediction
NMR,
Isomers
Tautomerization,Resonance, Stereoisomer
Conformation
Conformer, Molecular Dynamics, 3D Alignment
Geometry
Topology Analysis, Geometry, Polar Surface
Area (2D), Molecular Volume
Naming
IUPAC Names, Traditional Names
Other Hydrogen Bond Donor-Acceptor, Huckel Analysis,
Refractivity, Structure Frameworks
Structure based calculations are available from the Marvin
and Instant JChem GUI, cxcalc command line tool and the
API/ Available as functions of Chemical Terms expressions
Naming Technology
• Name to structure
– IUPAC, traditional and
common names
– A library of existing drugs
– Support CAS Registry
number
– Homology group: alkyl, aryl
…
– Future: Biological names
• Structure to Name
– IUPAC Name, traditional
names
• Accuracy and coverage
constantly improving
• Also available from
command-line
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ChemAxon’s “Document to Structure”
• Extract chemical
information from
documents – Names, SMILES, InChI,
CAS number …
– Structure images
– Works with scanned
non-searchable PDF
– Returns structures and
their location in the
document
– Correct OCR errors
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Non-searchable chemical patent
Structure (text + image) + location
JChem for SharePoint
• Add chemistry to SharePoint
2010 and 2007
• Manage, search and analyze
chemical structures in
SharePoint
– Sketch, Import/export, store,
search chemical structures into
SharePoint
– Calculate properties and naming
– Filtering and Sorting
• New improvement
– Index and search for documents
containing chemical (name)
information and embedded
chemical structures
– Connect SharePoint to your
chemical database
Our Most Important Assets
• Over 90 staff – 75% in development
– > quarter with PhD
– Organic growth
• Project managers by product line
• Support and commercial offices in USA,
UK, Romania, Czech republic. Japan,
China and India via partners
• Life style driven, no exit strategy (not
for sale)
©Patcore Inc. 2011 All Rights Reserved. Proprietary and Confidential
Introduction of CRAIS Database Management System for Life Science
Research Organization
Patcore, Inc.
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©Patcore Inc. 2011 All Rights Reserved. Proprietary and Confidential
CRAIS Series Overview
CRAIS Registration Compound Registration
System
Reagent DB
CRAIS Checker Controlled Substance
Detection System
Regulation DB
CRAIS Assay Assay Data Registration
System
CRAIS Browser Chem Bio Data
Browsing System
Assay DB
Powered by
SOAP Communication
Compound DB
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CRAIS Reagent Inventory Management
System
Third Party ELN
©Patcore Inc. 2011 All Rights Reserved. Proprietary and Confidential
CRAIS Registration and CRAIS Assay
• Web based compound related data registration system
• Build on ChemAxon JChem Cartridge and Standardizer
• Ability to integrate with other ChemAxon tools
– Structure Checker
– Structure to Name
– Physicochemical property calculation plugins
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CRAIS Registration CRAIS Assay
CRAIS Browser
Assay DB Compound DB
Compound Data Assay Data
©Patcore Inc. 2011 All Rights Reserved. Proprietary and Confidential
Registration Flow (Interactive Mode)
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Drawing
Property calculation (Optional) Regulation check (Optional) Calculation of MW Temporary registration
Standardization Error check
Duplicate check ID assignment
Approval
©Patcore Inc. 2011 All Rights Reserved. Proprietary and Confidential
CRAIS Browser
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Chemical and biological information Browsing system build on ChemAxon JChem Cartridge.
©Patcore Inc. 2011 All Rights Reserved. Proprietary and Confidential
Query Builder
Intuitive interface to build search query
Individual setting for search fields and display fields.
Store/share search queries.
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Search Domain Display Type
Searchable/Displayable Fields Search Conditions/ Display items
Ord
er o
f Disp
lay
©Patcore Inc. 2011 All Rights Reserved. Proprietary and Confidential
Result Display Types
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Table View
Grid View
Form View
Visit Other Technical Presentations
MarvinSketch/View http://www.chemaxon.com/MarvinSketch_View.ppt
MarvinSpace http://www.chemaxon.com/MarvinSpace.ppt
Calculator Plugins http://www.chemaxon.com/Calculator_Plugins.ppt
Chemical Naming http://www.chemaxon.com/conf/Naming.ppt
Structural Search http://www.chemaxon.com/Structural_Search.ppt
JChem Base http://www.chemaxon.com/JChem_Base.ppt
Markush Search http://www.chemaxon.com/conf/Markush_development.ppt
Instant JChem http://www.chemaxon.com/conf/Instant_JChem.ppt
JChem for Excel http://www.chemaxon.com/product/jc4xl.html
JChem Cartridge http://www.chemaxon.com/JChem_Cartridge.ppt
Standardizer http://www.chemaxon.com/Standardizer.ppt
Screen http://www.chemaxon.com/Screen.ppt
JKlustor http://www.chemaxon.com/JKlustor.ppt
Fragmenter http://www.chemaxon.com/Fragmenter.ppt
Reactor http://www.chemaxon.com/Reactor.ppt
• Product descriptions & links
www.chemaxon.com/products/
• Forum
www.chemaxon.com/forum
• Presentations and posters
www.chemaxon.com/library/
• Download
www.chemaxon.com/download
Find Out More