how to use this ppt template - chemaxon...tide1,peptide2,1:r3-1:r1$$$ correct tools used...
TRANSCRIPT
Budapest Annual Meeting
2016
BIOMOLECULE
TOOLKIT
Roland Knispel
www.amgenscience.com
Annual Meeting 2016
www.amgenscience.com
JChem
Annual Meeting 2016
www.amgenscience.com
JChem
Annual Meeting 2016
• API (Java and REST-ful) for
– Standardization
– Centralized DB storage
– Registration of entities and batches with custom
business logic
– Search by sequence/chemical structure/metadata
– Conversion to/from Mol/FASTA/HELM
– Property calculations
• Integrates with
– ChemAxon Instant JChem, planned: Plexus Suite
– Texelia BioScity, planned: IDBS E-WorkBook
Biomolecule Toolkit
Annual Meeting 2016
USE CASE: CHEMBL V21
• 19773 peptide
biotherapeutics with
associated activity data
• ChEMBL interface:
searchable by
CompoundID, chemical
structure or select
metadata
CHEMBL v21
Annual Meeting 2016
- KNIME
- Standardizer node
Ungroup S-groups, Strip
salts/solvents, Remove
explicit hydrogens, Neutralize
structure, Aromatize,
Standardize functional
groups
Tools used
Standardize Convert Canonicalize Store/Search
CHEMBL297610
Annual Meeting 2016
- KNIME
- Biomolecule Toolkit
- BioEditor for image
rendering
- 3 wrong
conversions in
ChEMBL data set
identified
Standardize Convert Canonicalize Store/Search
PEPTIDE1{E.C.G.[X1091]}$$$$
wrong
PEPTIDE1{E}|PEPTIDE2{C.G.[X1091]}$PEP
TIDE1,PEPTIDE2,1:R3-1:R1$$$
correct
Tools used
CHEMBL223118
Annual Meeting 2016
- KNIME
- Biomolecule Toolkit
- 864 HELM notations
in ChEMBL changed
- Allows direct
comparison of
HELM notations
Standardize Convert Canonicalize Store/Search
Tools used
Before:
PEPTIDE1{[ac].[dE].[Phe(4-Cl)].[d3-
Pal]}|PEPTIDE2{D.R.[dNal].L.K}|PEPTID
E3{P.[dDpr].[am]}$PEPTIDE2,PEPTIDE3
,5:R2-1:R1|PEPTIDE2,PEPTIDE1,5:R3-
2:R3|PEPTIDE1,PEPTIDE2,4:R2-
1:R1|PEPTIDE3,PEPTIDE2,2:R3-
1:R3$$$
Before:
PEPTIDE1{G.Y.G.F}$PEPTIDE1,PEPTID
E1,4:R2-1:R1$$$
After:
PEPTIDE1{F.G.Y.G}$PEPTIDE1,PEPTID
E1,4:R2-1:R1$$$
After:
PEPTIDE1{[ac].[dE].[Phe(4-Cl)].[d3-
Pal].D.R.[dNal].L.K.P.[dDpr].[am]}$PEPTI
DE1,PEPTIDE1,11:R3-
5:R3|PEPTIDE1,PEPTIDE1,9:R3-
2:R3$$$
CHEMBL412009
CHEMBL42623
Annual Meeting 2016
- Biomolecule Toolkit
Search by:
- Sequence (incl.
wildcards)
- Chemical structure
- Modifications
- Metadata
Standardize Convert Canonicalize Store/Search
Tools used
Query # hits
Molecules containing „Oxytocin“ in name field2
Molecules with the natural analogue
sequence of Oxytocin18
Oxytocin-like sequences with non-standard
amino acids17
Oxytocin derivatives containing the chemical
structure of penicillamine3
Oxytocin derivatives containing the L-
penicillamine monomer2
Annual Meeting 2016
BIOMOLECULE TOOLKIT AS A PLATFORM
Registration DB
Biomolecule Toolkit API
Registration
ClientInstant JChem
Plexus
Connect
Data Access Layer
JChem for
Office
REST Web Service Layer
Architecture
Annual Meeting 2016
- Create new project
pointing to
Biomolecule Toolkit DB
- Grid view with
molecule visualization
New: Biomolecules in Instant JChem
Annual Meeting 2016
- Create new project
pointing to
Biomolecule Toolkit DB
- Grid view with
molecule visualization
- Form views with
additional data
- Querying
New: Biomolecules in Instant JChem
Annual Meeting 2016
Following talk by Dominique Besson
Texelia BioScity - Data management/tracking and inventory for the Bio/Chem lab
Annual Meeting 2016
INTRODUCING A FULLY WEB-BASED
TOOL FOR DRAWING BIOMOLECULES
- Easy structure/
sequence editing
- Supports no-structure
components
- Multi-level
annotations
- Clear visualization
- Customizable views
- JS application
Coming this summer: BioEditor*
*working title
Annual Meeting 2016
- Standalone
- Bundled with
Biomolecule Toolkit
Beta tests running now
Contact biotoolkit-
to sign up
Product release in summer
Coming this summer: BioEditor*
*working title
Annual Meeting 2016
ROADMAP
Q2 2016
• XHELM/HELM2 support for structurally ambiguous entities in Biomolecule Toolkit and BioEditor*
• Switch to JS from Java applets
Q3/4 2016
• Biomolecule support in Plexus Suite
• Rule-based bulk import/editing of biomolecules
• BioEditor* product release
2017
• Design/developability assessment/SAR analysis
• Biomolecule support in JChem for Office applications
Roadmap
*working title
Annual Meeting 2016
SUMMARY
Summary
• Curation and standardization of existing
content
• Structure management á la JChem/Marvin
including registration
• Biomolecule and bio-asset data
management platform for desktop and web
Annual Meeting 2016
THANK YOU