CHEMAXON PORTFOLIO WALK THROUGH · CHEMAXON PORTFOLIO ... -JChem PostgreSQL Cartridge support...

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CHEMAXON PORTFOLIO WALK THROUGH From toolkits to end-user applications to deliver solutions Aurora Costache, PhD

Transcript of CHEMAXON PORTFOLIO WALK THROUGH · CHEMAXON PORTFOLIO ... -JChem PostgreSQL Cartridge support...

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CHEMAXON PORTFOLIO –

WALK THROUGHFrom toolkits to end-user applications to deliver

solutions

Aurora Costache, PhD

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WHO WE ARE

Hungarians

Romanians

Iranians

Nigerian

Czechs

Hawaiian

Americans

Ukrainians

French

Canadian

PolishSerbians

Indians

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Budapest, Hungary – Prague, Czech Republic - Cambridge, MA USA

Locations

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How we work…

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How we do meetings…

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How we are listening to our clients…

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How we have fun…

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Pharmaceutical and

Biotech Industry –

Drug Discovery

• Small molecules

• Biological entities

General

Chemistry

Polymer

Chemistry

Petrochemistry

Agrochemistry Flavors and Fragrances

Academia

Cheminformatics leaders, since 1998, solution providers

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Two faces of one world

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• Tests – improved and evolving

• Feedback

• Weekly releases

Committed to quality

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CHEMAXON PORTFOLIO

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Fate of a compound

Create

Store

Analyse

Publish

Sketch/Convert

/Import

Register/Index

Query/Display

Reports

Assay data, Experience

accumulationComprehend Outcome

Synthesize, Purchase,

CollectKnowledge,

Vision

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Fate of a compound

Create

Sketch/Convert

/Import

Knowledge,

Vision

Naming/Annotating

ChemCurator

ChemLocator

Chemicalize

Design/Sketchers

Marvin/Marvin JS

BioEddie

Property Calculations

Reactor/Plexus Design

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Creating chemical content with Best drawing tools on the market!

MarvinSketch Marvin JS

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MarvinSketch

- Advanced

chemical editor

- Publication

quality drawing

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Marvin JS

Concept Mastery

Reaction Explorer

End of

Chapter/Testbank

Homework

and test preparation

Chemistry Education

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Industry Standard

Marvin JS

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Drawing and viewing complex molecules in your browser

BioEddie

• Fully characterized to fully

unknown

• Exact chemical descriptions

to heterogeneous products

• Biological sequences to

exotic bioconjugates

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Property calculators

An analysis of the attrition of drug candidates from four major pharmaceutical

companies (AstraZeneca, GlaxoSmithKline, Pfizer, Eli Lilly)

„A set of physicochemical descriptors was independently calculated for these

compounds by each company using ChemAxon 5.9 (see Further information) to

provide a consistent set of descriptors.”

Nature Reviews Drug Discovery 14, 475–486 (2015)

High-quality predictions

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Powerful lead generation and lead optimization engine

Property calculators

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Reactor

Reactants

REACTOR

Baeyer-Villiger ketone oxidation

Baylis-Hillman vinyl alkylation

Beckmann rearrangement

Bischler-Napieralski isoquinoline synthesis

Friedel-Crafts reaction

Friedlander quinoline synthesis

Gabriel synthesis

Grignard reaction

Hell-Volhardt-Zelinski halogenation

Products

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In Instant JChem

Reactor

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In JChem for Excel

Reactor

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In Plexus Suite – Plexus Design

Reactor

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Naming Suite

(2-butyl-4-chloro-1-

{[2'-(2H-1,2,3,4-

tetrazol-5-yl)-[1,1'-

biphenyl]-4-

yl]methyl}-1H-

imidazol-5-

yl)methanol

losartan

hyzaar

cozaar

lortaan

Lozartan

clopidogrel

114798-26-4

IUPAC names

Chemical strings

Generic structures

Simple structures

Tautomeric forms

Salt forms

pdf

html

xls

docx

pptx

CAS Numbers

OLE objects

Trivial namestext

Internal ID-s

A reliable chemical name conversion and mining engine

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Document annotation

Naming Suite

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ChemCurator

Compound list

Project explorerAnnotated document

Selected structures

Computer-Assisted Document Curation and Analysis –

Compound Extraction View

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Markush editor

Example structures

Annotated document

Selected structures

Structure checker

ChemCuratorComputer-Assisted Document Curation and Analysis –

Compound Extraction View

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Markush Editor

- Handling complex Markush

structures

- Markush drawing and visualization

- Enumeration

- Automatic Markush generation

(composer)

- Real time interactive analysis

against stucture lists

(hit and non-hit visualization)

Toolkit for the analysis of virtual combinatorial library and patent Markush

structures

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C:\\

Shared Directories

ChemLocator

in

JChem

Chemical Search in Unstructured Data

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Fate of a compound

Store

Register/Index

Synthesize, Purchase,

Collect

Compound/Project

Management

Marvin Live

Compliance Checker

Instant JChem

Compound Registration

Biomolecule ToolkitAssay data, Experience

accumulation

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Molecule Design and Idea Management

Marvin Live

Rigid alignment

70 + plugins

(ChemAxon + 3D party)

- Flexible interface

- Harmonized CADD and

design capabilities

- Predictive models

- Databases

- CXN Calculated

properties

- 3D alignment

- Protein surface

visualization

- Reaxys

- KNIME

- Pipeline Pilot…

Create, collect, challenge

ideas in a project

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- Combined software system and

content package

- Provide ways to check whether

compounds are controlled

according to the relevant laws of

the countries of interest

Compliance Checker Stay out of jail!

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Coverage/Accuracy

Country Pass Rate

Canada 100%

France 100%

USA 99%

UK 99.7%

Sweden 100%

Switzerland 100%

Compliance Checker

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• Create, explore and share

chemical and non-chemical data

in local and remote databases

without additional administration

Instant JChemInstant JChem

Desktop application for DB management

to create, explore and share data

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Key features

- Advanced query builder

- List management, domain search

- Customizable database views - form designer

- Integration of library enumeration

- Molecular property and descriptor predictions

- Charting options

- Scripting for extension and customization

- Data pivoting

- New Molecule Matrix

- Biomolecule Toolkit integration

- JChem PostgreSQL Cartridge support

Instant JChemDesktop application for DB management to create, explore and share data

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Compound Registration

• Hierarchical storage

o Parent structures

o Salt/solvate forms

o Batches/lots

• Multi-component

structures

• Markush structures

Parent

Version 1

Batch 1

Batch 2

Version 2 Batch 3

The best registration system on the market!

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API (Java and REST-ful) for

– Native HELM support (HELM, HELM2, xHELM)

– Standardization

– Centralized DB storage

– Registration of entities and batches with custom

dbusiness logic

– Search by sequence/chemical structure/metadata

– Conversion to/from Mol/FASTA/HELM

– Property calculations

Biomolecule ToolkitBridge the gap between biology and chemistry

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Biomolecule ToolkitBridge the gap between biology and chemistry

Integrates with

–Since v16.8.1: Instant JChem, planned: Plexus Connect

–Texelia BioScity, planned: IDBS E-Workbook

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- Store

- Index

- Search

- unambiguous representation

at sequence and atomic level

for a diverse set of

biomolecules:

- peptides

- oligonucleotides

- proteins

- antibody drug conjugates

- including those containing

unnatural and chemically-

modified components

Biomolecule ToolkitBridge the gap between biology and chemistry in Instant JChem

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Fate of a compound

Analyse

Query/Display

Comprehend

Store, Search and

Display

JChem Suite (Base +

Cartridges)

MadFast SS

Plexus Suite

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The heart of ChemAxon:

Fast, invisible chemical backend you can rely on.

Index, search and manage data: The best chemistry engine on the market!

JChem Base

Instant JChem

Plexus ConnectCompound Registration

Compliance Checker

JChem Web Services

JChem for Excel JChem for SharePoint

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JChem CartridgesMakes databases chemically intelligent: Oracle - PostgreSQL

Fast chemical searches

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Plexus SuitePlexus Connect: Instant data access for end-users on any web browser

- The discovery user

interface

- Access, Display and

Query scientific data

- Web-based, thin

client interface

- Instant JChem for

administration, form

building

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Plexus Analysis: Find the needle in the haystack

Curve fitting

Linear regression

Easy and fast datasets correlations

Plexus Suite

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MadFast Similarity SearchFaster similarity based search, overlap analysis and clustering

Fast similarity search and overlap analysis

Multiple datasets

● Real time similarity

searches

● Similarity based overlap

analysis of large sets

● Similarity search on

extremely large datasets

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Fate of a compound

Publish

Reports

Outcome

Report

JChem for Office

Instant JChem

Marvin Live

Plexus Suite

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JChem for OfficeMicrosoft Office applications (Excel, Word, PowerPoint, Outlook) with chemical

intelligence

Practical and effective chemical data analysis and reporting tool

Direct data channeling from relational databases, Instant JChem or chemical

data files

Easy usage, in a known milieu: optimal learning curve with minimal cost of

education

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- Property calculations

- R-group decomposition

- Substructure search

- Reaction-based enumeration

- SAR-matrix generation

JChem for Office

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Reporting and presenting

JChem for Office

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and Marvin Live

Instant JChem

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Plexus Suite

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Summary Mine

Create

Register

Comprehend

Publish

Naming/Annotating

Chem Curator

ChemLocator

Chemicalize

Design/Sketchers

Marvin/Marvin JS

BioEddie

Property Calculation

Reactor/Plexus Design

Compound/Project

Management

Marvin Live

Compliance Checker

Compound Registration

Biomolecule Toolkit

Instant JChem

Store, Search and

Display

JChem Suite (Base +

Cartridges)

Plexus Suite

JChem for SharePoint

MadFast SS

Report

JChem for Office

Instant JChem

Marvin Live

Plexus Suite

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CHEMAXON PORTFOLIO

Future Plans

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55

CompReg

Assay (Inventory)

ChemAxon

Synergy

DISCOVERY

DATA CAPTURE

3rd PARTY TOOLS

Workflow Tools

Modelling

SAR reports

Query, Report

Data Analysis

Ontology

Integrated 3rd party tools

and POCs

Design

IJC/Connect Analysis

Registration

ELN

Inventory

ChemAxon Synergy as a platform

Compliance Checker

Marvin Live

ChemLocator

ChemAxon supporting

tools

Consultancy

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Agenda

- Presentations of ChemAxon solutions from Product

Owners and Consultancy

- ChemAxon solutions from our clients

- Tools and solutions from our partners

- Demo stations:

- talk with Product Owners

- hands-on tools and solutions

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THANK YOU

Aurora Costache, PhD