1. Roland Knispel
Bioeddie

2. BioEddie JS application for all major browsers Easy editing
No-structure components
Native support for MOL/HELM/sequence
Customizable views
Multi-level annotations

3. New in BioEddie
Highlight monomers with free attachment points when drawing bonds
Append/prepend/insert monomers to sequences
Add/edit domain annotations
Display chemical structure of molecule
Scrollbars when molecule does not fit on canvas

4. In the pipeline Expand monomers on canvas
More UX and productivity improvements
Multi-selection

5. Roland Knispel
Biomolecule Toolkit

6. Biomolecule Toolkit API (Java and REST-ful) for
Native HELM support (HELM, HELM2, xHELM)
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
Main message
We provide a machine readable format for the unambiguous description of biomolecules. We support fully and partially defined biomolecules. We have full metadata support, which is a lot more relevant for biomolecules than for small molecules.
Notes
You may be asked here if we support random polymers. The Toolkit is not aimed at solving the description of random polymers (e.g. dendrimers etc.). Mention this here only if it is asked.

7. New in Biomolecule Toolkit
Experimenting with BioJava for adding bioinformatics capabilities
Compatible with Java 8 and higher
Improvements in MOL2HELM conversion
Improved HELM2 support
Registration of non-structure entities (Cell lines, viruses and other bio-assets)

8. In the pipeline Lot level handling Improved annotation handling
Genealogy capture
Application security (authentication, role-based authorization)
Goal: Establish Biologics registration solution on par with Compound Registration

9. Use case
Informatics support for peptide discovery

10. SAR-driven design* How to make transition seamless
How chemist refines structure
Original
Modified
How SAR is performed
*See Joshua Bishop, Merck (MSD), UGM presentation, 2017, San Francisco

11. Biomolecule Toolkit Integration at Heptares*
Registration of peptides in CTAB format
CTAB generated via interconversion of HELM strings
Error-prone manual drawing of peptides by users
Drastic reduction of errors in database registration
At the core of curated database of peptide and chemical monomers
~400 Amino acid residues
~200 Chemical groups
Manual Curation via ChemAxon Biomolecule Toolkit RESTful API and BioEddie
Monomer DB
HELM Generation
Sequence Analysis
MOL Block
current
Molecule Registration
Molecule Display
Library Enumeration
planned
*See Conor Scully, Heptares, UGM presentation, 2018, Budapest