What is the Biotoolkit Monomer Service?
The Biotoolkit Monomer Service is the monomer library behind Discngine's biologics tools. It stores the building blocks that HELM sequences refer to by symbol: natural and non-natural amino acids, nucleotides, and chemical linkers, each with its structure, its attachment points and its cap groups.
Discngine applications resolve every symbol of a peptide against this library, and a peptide whose symbol is unknown has no structure until the monomer is registered here. The Biotoolkit Monomers web application is where your organisation curates that library.
The application has four pages, listed in the navigation menu on the left:
| Page | What it is for |
|---|---|
| Home | A dashboard: whether the Biotoolkit services are up and the library in sync, how many monomers the catalogue holds, what changed recently, and the quick actions. |
| Monomers | The catalogue itself: one row per monomer with its drawing, filter chips by scope, polymer type and stereochemistry, plus the N-terminal or C-terminal position once Peptide is selected, and the New monomer and Import a file buttons. |
| Aliases | The other names monomers answer to in HELM, yours and the public ones. |
| Version history | For Administrators: every earlier state of your organisation's monomers, and the deletions you can undo. |
Key capabilities
- Two layers of monomers: a public reference library shared by every organisation, read-only, and your organisation's private monomers, which you create and maintain.
- Structure-first registration: a monomer is defined by its SMILES with numbered attachment points. The application draws it before you save, and derives the R-groups from the structure.
- Bulk import: load a CSV, Excel or SDF file of monomers, follow the import in the import history, and download an error file for the rows that failed.
- A browsable catalogue: the Monomers page shows every monomer with its drawing, narrows the list with chips and filters on any column, counts the catalogue overall and per polymer type, and opens any drawing full size in a structure viewer.
- Duplicate detection: the same structure cannot be registered twice within a polymer type, and a private monomer cannot shadow a public one.
- Aliases: a monomer can answer to several names, so sequences written with your naming convention resolve to the same monomer, public ones included, instead of creating duplicates.
- Full history: every material change and every deletion is archived. An Administrator can compare the before and after of an edit, and put a deleted monomer back.
Roles
Access is granted per organisation, with one of three roles:
| Role | What it allows |
|---|---|
| Viewer | Browse the public library and your organisation's monomers, open a monomer to read its definition and structure, download the reports. Nothing can be changed. |
| Manager | Everything a Viewer can do, plus registering monomers: create and edit private monomers on the form, import them in bulk, and add or remove your organisation's aliases. |
| Administrator | Everything a Manager can do, plus deleting monomers, reading the Version history and reviving deleted monomers. |
Everything you create is visible to your organisation only. Its name is shown in the top bar of the application.
Guides
| Guide | Audience | Description |
|---|---|---|
| How to Create or Edit a Monomer | Managers | Register a monomer from its SMILES, preview the structure, set the cap groups |
| How to Import Monomers in Bulk | Managers | Load a file of monomers and fix the rows that failed |
| How to Manage Monomer Aliases | Managers | Give a monomer other names, remove them, add them in bulk |
| How to Review a Monomer's Version History | Administrators | Read the Version history and revive a deleted monomer |
| Public Monomers | Everyone | Why some monomers are read-only, and how they relate to yours |
| Monomer Aliases | Everyone | What an alias is, its scope, and the rules that keep every name unambiguous |
| Monomer Types, Polymer Types and Natural Analogs | Everyone | What the classification fields mean and how they constrain each other |
| Attachment Points and CAP Groups | Everyone | How R-groups are written in SMILES and what a cap group is |
| Versioning and Deletion | Everyone | What counts as a new version, and what deleting really does |
| Canonical SMILES and Duplicate Detection | Everyone | How the service decides that two monomers are the same |
| Import File Format | Managers | Every column of the import file |
| Release Notes | Everyone | What changed in each release |