Post on 22-Jul-2020
CHEMAXON PORTFOLIO –
WALK THROUGHFrom toolkits to end-user applications to deliver
solutions
Aurora Costache, PhD
WHO WE ARE
Hungarians
Romanians
Iranians
Nigerian
Czechs
Hawaiian
Americans
Ukrainians
French
Canadian
PolishSerbians
Indians
Budapest, Hungary – Prague, Czech Republic - Cambridge, MA USA
Locations
How we work…
How we do meetings…
How we are listening to our clients…
How we have fun…
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
• Tests – improved and evolving
• Feedback
• Weekly releases
Committed to quality
CHEMAXON PORTFOLIO
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
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
Creating chemical content with Best drawing tools on the market!
MarvinSketch Marvin JS
MarvinSketch
- Advanced
chemical editor
- Publication
quality drawing
Marvin JS
Concept Mastery
Reaction Explorer
End of
Chapter/Testbank
Homework
and test preparation
Chemistry Education
Industry Standard
Marvin JS
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
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
Powerful lead generation and lead optimization engine
Property calculators
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
In Instant JChem
Reactor
In JChem for Excel
Reactor
In Plexus Suite – Plexus Design
Reactor
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
html
xls
docx
pptx
CAS Numbers
OLE objects
Trivial namestext
Internal ID-s
A reliable chemical name conversion and mining engine
Document annotation
Naming Suite
ChemCurator
Compound list
Project explorerAnnotated document
Selected structures
Computer-Assisted Document Curation and Analysis –
Compound Extraction View
Markush editor
Example structures
Annotated document
Selected structures
Structure checker
ChemCuratorComputer-Assisted Document Curation and Analysis –
Compound Extraction View
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
C:\\
Shared Directories
ChemLocator
in
JChem
Chemical Search in Unstructured Data
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
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
- 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!
Coverage/Accuracy
Country Pass Rate
Canada 100%
France 100%
USA 99%
UK 99.7%
Sweden 100%
Switzerland 100%
Compliance Checker
• 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
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
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!
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
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
- 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
Fate of a compound
Analyse
Query/Display
Comprehend
Store, Search and
Display
JChem Suite (Base +
Cartridges)
MadFast SS
Plexus Suite
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
JChem CartridgesMakes databases chemically intelligent: Oracle - PostgreSQL
Fast chemical searches
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
Plexus Analysis: Find the needle in the haystack
Curve fitting
Linear regression
Easy and fast datasets correlations
Plexus Suite
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
Fate of a compound
Publish
Reports
Outcome
Report
JChem for Office
Instant JChem
Marvin Live
Plexus Suite
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
- Property calculations
- R-group decomposition
- Substructure search
- Reaction-based enumeration
- SAR-matrix generation
JChem for Office
Reporting and presenting
JChem for Office
and Marvin Live
Instant JChem
Plexus Suite
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
CHEMAXON PORTFOLIO
Future Plans
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
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
THANK YOU
Aurora Costache, PhD