Transcript ChemAxon Presentation

Solutions for Cheminformatics
Company and product overview
September 2009
ChemAxon fingerprint
• Founded in 1998, based in Budapest,
Hungary
• Representation in Europe, US, Japan and
China
• Wide industry reach >320 corporate clients
• >2600 Academic Package subscribers
• Wide expertise, critical mass (~50 staff) 15
PhD, 35 MSc
Product Map
Active across the Globe
Active across the Globals
ChemAxon Embedded - examples
• Workflow
– Pipeline Pilot, InforSense KDE, and KNIME
• ELN
– Agilent, Contur, DeltaSoft, Kinematik, etc.
• SAR
– Spotfire, Synaptic Science, Omniviz
• Databases
– Aureus, GVK, Jubilant Biosys
• Registration System
– Patcore, Deltasoft
• Web content
– Thomson Reuters, Wiley, Houghton Mifflin, Cengage,
Prentice Hall, Collaborative Drug Discovery, RCSB PDB,
BindingDB, NIH/NLM ChemIDPlus, Molport etc.
The ChemAxon Advantage
•
Comprehensive
– Visualisation /drawing, data
management, drug discovery
– From toolkit to fullkit
•
•
Compatible
– Mutliple platform support on all
products
– Customizable to own needs
– API – Java, .NET, SOAP
– Common core across all products
Interface
– Intuititive “as you like it” GUI
– Easy to adopt/adapt
•
Performance
– Scalability
– Speed
•
Quality
– Best in class products
– Customer developed and tested
•
Support
– Rapid response (within 24 hr)
– Project and integration
management
•
Experience
– 11 years cheminformaniacs
– Development projects with
biotech, chem services and
publishers
– Dozen successful migration
projects
MarvinSketch/View http://www.chemaxon.com/MarvinSketch_View.ppt
MarvinSpace
http://www.chemaxon.com/MarvinSpace.ppt
The Marvin family
MarvinSketch
MarvinView
MarvinSpace
Available as applets for HTML pages and components for standalone apps (full API)
Structure, query &
reaction editing
Individual and
structure table
visualization
Macromolecule
visualization
Marvin Development History
1998
1999
2000
2001
2002
2003
Applets,
Molfiles, stereo
support,
Windows,
Unix
SDF, RDF, XYZ
animations,
CML, templates,
compressed
formats, Swing,
3D models
SMILES,
SMARTS,
PDB,
Rgroups,
isotopes,
shortcuts,
Marvin
Beans
Ball and stick
JPG, PNG, SVG,
Cut&Paste with
Isis/ChemDraw,
2D cleaning,
(de)aromatization,
reaction drawing
Mac
support,
signed
applets,
Java Web
Start, atom
mapping
Partial charge,
pKa, logP/logD,
3D optimization,
radicals,
abbreviated
groups
2004
2005
2006
2007
2008
Marvin file format,
enhanced
stereo, shapes,
text boxes,
multiple groups,
link nodes, TPSA,
recursive
SMARTS,
Donor/Acceptor,
electron arrows,
Tautomers,
resonance, lone
pairs,
conformers, 3D
sketching,
MarvinSpace,
More Plugins,
more R-groups,
EMF, PDF and
Mol2,
Improved
property storage
in MRV, SDfiles
and Rdfiles.
.NET support in
MarvinBeans.
Structure to
name,
Coordination
compounds,
Polymer
drawing, OLE,
Markush
enumeration
plugin
Configurations
Transparent
Name to
structure, OLE images
.NET
2,
Chemical Terms, Applet loading
Customizable speed up
Sprout drawing
GUI
Topology
analysis,
presentation
quality
graphics,...
2009
Calculator Plugins http://www.chemaxon.com/Calculator_Plugins.ppt
Calculator Plugins
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.
Elemental Analysis
Structure to Name
Protonation
pKa, Major Microspecies, Isoelectric Point
Partitioning
logP, logD
Charge
Charge, Polarizability, Orbital Electronegativity
Isomers
Tautomerization,Resonance, Stereoisomer
Conformation
Conformer, Molecular Dynamics, 3D Alignment
Geometry
Topology Analysis, Geometry, Polar Surface
Area (2D), Molecular Surface Area (3D)
Markush enumeration
Other
Hydrogen Bond Donor-Acceptor, Huckel Analysis,
Refractivity, Structure Frameworks
Chemicalize the Web: http://www.chemicalize.org/
Chemical Naming
Structure to Name/ Name to structure
Supported nomenclatures :
• Chains, Monocycles/ Traditional names with
and without heteroatom/ Spiro ring systems/
Ethers/ Common characteristic groups, Ionic
compounds/ Unlimited number of atoms
and rings/ All atom types /Stereochemistry/
etc.
Usage:
• drag&drop or copy&paste to MarvinSketch
• Label updated in real-time
• Automatic format recognition
• Batch from command line
• Name to structure conversion of documents
• www.chemicalize.org
JChem family
JChem Base
JChem Cartridge Instant JChem
JChem for Excel
API for structure
searching and
database handling
Tight Oracle SQL
integration
Desktop application
for scientist
Marvin and JChem
functionality
Available from Java,
.NET and Web
services
SQL functions for
chemistry
Access local and
remote databases
Excel functions,
sorting, filtering,
charge etc…
JChem development history
2000
2001
2002
2003
Oracle, MySQL,
SQLServer,
Access, hashed
fingerprints,
substructure
and similarity
search
Clustering,
diversity
DB2, PostgreSQL, Reaction searching,
Rgroup searching fragmentation,
reaction processing,
standardization,
pharmacophores,
screening
2004
Cartridge, enhanced
stereo searching,
recursive SMARTS,
Chemical Terms,
virtual synthesis
2005
2006
2007
2008
R-decomposition,
R-enumeration,
reaction library,
custom fingerprints,
random synthesis,
link nodes…
Tautomer search,
Instant JChem
reaction similarity,
Library MCS, GUI
for Standardizer/
Reactor …
Calculated columns,
Installer,
Tautomer Duplicate
filtering, Query
tables, Markush
tables, Speed
Position variation
JChem for Excel
queries,
JChem Web
Instant JChem:
Services, AJAX
-- Federated search,
Polymer search
-- Cartridge
Data Sgroup search
support...
Faster SSS
enhancements for
JChem Cartridge,
form design,
relational data for
Instant JChem ...
2009
Metabolizer
Structural Search http://www.chemaxon.com/Structural_Search.ppt
JChem Base http://www.chemaxon.com/JChem_Base.ppt
JChem Base
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 and AJAX open source web examples
• Desktop-ready through Instant JChem
• JChem Web Services available
DB2
Searching in combinatorial Markush structures
Combinatorial Markush structure registration and search
• Markush features handled in search &
enumeration:
― R-groups (nesting to any depth)
― Atom lists, bond lists
― Position variation bond
― Link nodes and repeating units
― Homology groups
• Compatible Markush enumeration plugin
• Not all query features supported
Detailed description:
http://www.chemaxon.com/product/markush_search.html
JChem Cartridge http://www.chemaxon.com/JChem_Cartridge.ppt
JChem Cartridge for Oracle
• Access JChem functionality via SQL functions
• All search features of JChem Base
• JChem index for chemical data in arbitrary database structure
• Chemical filters and property predictors using Chemical Terms
• Standardization (structure canonicalization) during registration
• Structure format conversions
• 2D, 3D image generation
• Library enumeration using
virtual reactions and
Markush structures
Instant JChem: http://www.chemaxon.com/conf/Instant_JChem.ppt
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 (106 +)
• Dynamically predict properties
using Calculator Plugins
• Apply canonicalization rules for
import and viewing
• Wide import / export options
• Merge data sets into a single
set
JChem for Excel
•
Microsoft Excel integrated
solution for Marvin and JChem
functionality
•
Use 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
JChem Web Services Server
•
Web Services integration of
JChem functionality
― JChem Search
― Molecular Conversion
― Standardizer
― Chemical Terms
•
Enables SOAP capable (e.g.
AJAX, Perl, Python)
programming environments
•
Standalone server
― Chainable with other web
services
•
Easy to install and deploy
Standardizer http://www.chemaxon.com/Standardizer.ppt
Canonicalization with Standardizer
• Structure canonicalization
–
–
–
–
–
–
–
–
–
Mesomers
Tautomers
Solvent and counter ion removal
Aromatization, dearomatization
Explicit/implicit hydrogen conversion
Stoichiometry expansion
Stereo manipulations
2D cleaning
Template based cleaning
• Custom rules
• Structure checker
• Availability
– JChemBase
– API
– Batch processing
Drug discovery tools
JKlustor
Screen
Profiling, analysis, diversity
Virtual screening by topological
descriptors
Fragmenter
Reactor
Library profiling and reactant
generation
Virtual reactions and synthesis
Screen http://www.chemaxon.com/Screen.ppt
Virtual Screening with Screen
• Active set dependent automated optimization
• Wide range of descriptors
– native chemical fingerprint
– pharmacophore fingerprint
• customizable definitions
• functional group based mapping
• calculation based mapping
– calculator plugins
– user defined descriptors
– combined descriptors
• Tanimoto and Euclidean metrics
– Tunable parameters
•
•
•
•
normalization
weighting
scaling
directing (asymmetric)
JKlustor http://www.chemaxon.com/JKlustor.ppt
Clustering with JKlustor
• Similarity and structure based, Hierarchical
and non-hierarchical methods
– hierarchical
• Ward
• MCS
– non-hierarchical
• Jarvis-Patrick
–
–
–
–
Chemical fingerprint
Pharmacophore fingerprint
Calculator plugins
User defined custom descriptors
Running time (min)
• Wide range of descriptors
Clustering performance comparison
90
80
70
60
50
40
30
20
10
0
LibraryMCS
Jarvis-Patrick
Ward-Murtagh
0
20000
40000
60000
80000
Input structure count
100000
120000
Fragmenter http://www.chemaxon.com/Fragmenter.ppt
Library profiling with Fragmenter
•
Transformation based fragmentation
method
–
–
–
–
–
–
–
•
•
Customizable transformations
RECAP transform set
Synthetically relevant transformations
Labeled connections
Options to keep fragment feasible
(no ring opening, limit fragment size, limit the number of
connection points, etc)
Fragment statistics
Activity based scoring
High throughput fragmentation
•
Simple rule cleaving carbon-carbon single bond next to a hetero
atom (CCQ)
•
Functional groups remain intact
•
Very fast algorithm (no ring
perception, no substructure
search)
R-group decomposition
Virtual Synthesis with Reactor
• Reaction Engine
– Converts reactants according to a given reaction scheme
– Chemo-, regio- and stereospecific reactions are supported by
the integrated property calculation functions (if the reaction
contains rules in Chemical Terms format).
– Compatible with the popular molecule, reaction file and reaction
mapping formats.
• Reactor Application
– An application of the
reaction engine for
combinatorial chemistry.
– Wizard-like application
and reaction editor.
– Built in testing system.
Metabolizer
Virtual reaction based metabolite
enumeration tool
 xenobiotic metabolic pathways
prediction
 metabolic stability
 metabolically sensitive groups and
major metabolites
 can be customized by various
biotransformation libraries
 Human phase I, xenobiotic CYP450
biotransfomation library UNDER
DEVELOPMENT
Under Development
•
Integration of Screen descriptors and metrics into Cartridge
•
Structure Checker for Standardizer
•
Marvin GUIs to be added to the .Net API
•
New features for Instant JChem, like multi tier architecture, improved
reporting capabilities, improved visualisation
•
Improve Markush structure handling in JChem Base / Cartridge / Marvin
•
JChem for Excel
•
Metabolite and metabolic stability prediction
•
Human CP450 biotransformation library
•
Multistep reactions in Marvin and JChem
•
Compound registration system
• 3D similarity searching based on flexible alignment
•
SKC support
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
Find out more
• Product descriptions & links
www.chemaxon.com/products.html
• Forum
www.chemaxon.com/forum
• Presentations and posters
www.chemaxon.com/conf
• Download
www.jchem.com/licensefrset.html