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

Active across the Globe

Product Map

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

Database Management Application

JChem for Excel

Instant JChem

6

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

9

Reactor

Markush

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

12

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

14

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

15

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.

18

©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

19

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

20

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)

21

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

22

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.

23

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

24

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