This guide covers importing a peptide dataset from a HELM file (CSV/Excel) or an SDF, supplying a monomer library, and configuring peptide-specific options.
The Peptide dataset type is only available when the peptide plugin is enabled for your organization. If you do not see it, contact your administrator.
Step 1: Open the New Dataset wizard
From the Home page, click the Create Dataset card (or New → Create Dataset in the left navigation). The New Dataset wizard opens with three steps: Dataset Information, Properties Configuration, and Import Status.
Step 2: Choose the Peptide dataset type
Under Dataset Type, select Peptide.
Then choose the target Project and the Dataset File.
Accepted file formats for peptides:
| Format | Notes |
|---|---|
CSV / Excel (.csv, .csv.gz, .xlsx) |
Tabular files with an identifier column and a HELM column; every other column becomes a property. HELM references monomers by symbol only, so a monomer library is needed for any monomer not already in the Biotoolkit Monomer Service. |
SDF (.sdf, .sd, .sdf.gz, .sd.gz) |
A V3000 SDF that carries the peptides and a monomer template for each monomer. The embedded templates are used to register any missing monomers on the Biotoolkit Monomer Service, so no separate monomer library is needed. |
Use the Download peptide dataset templates links (CSV / Excel) in the dialog to start from a correctly formatted file. The template's columns are ID, HELM and three example property columns, so a minimal row looks like PEP001,PEPTIDE1{A.G.K.L}$$$$.
Step 3: Supply a monomer library (CSV/Excel imports only)
A Monomer Library File maps each monomer symbol to its chemical structure so Ideation can register monomers that are not yet in the Biotoolkit Monomer Service. It is needed only for CSV/Excel (HELM) imports — HELM references monomers by symbol without carrying their structures — and the picker appears only for those files.
It can be a CSV, Excel, or SDF file, and it uses the same field names as the Biotoolkit Monomer Service import template — so a library file written for the Biotoolkit Monomer Service imports into Ideation unchanged, and vice versa.
| Field | Required | What it holds |
|---|---|---|
symbol |
yes | The symbol the HELM sequences use. |
smiles |
one of | The structure as SMILES, with numbered attachment points — C[C@H](N[*:1])C([*:2])=O. |
ctab |
one of | The structure as a connection table. For an SDF, the molfile itself is the structure and no ctab field is needed. |
name |
no | Falls back to the symbol. |
polymer_type |
no | PEPTIDE or CHEM. Inferred from how the dataset's HELM uses the monomer when absent. |
monomer_type |
no | Backbone or Undefined. |
natural_analog |
no | The natural amino acid the monomer stands in for. |
rgroups |
no | The attachment points and their cap groups, as R1:H;R2:OH. Derived from the structure when absent. |
author |
no | Accepted for compatibility with the Biotoolkit Monomer Service template; not stored. |
Each row needs a symbol and a structure — either smiles or ctab. A row with neither is rejected by name rather than skipped silently. Columns Ideation does not know are ignored, so extra columns are never a reason for a file to fail.
polymer_type, monomer_type and rgroups are the fields Ideation can work out on its own — but when your file states them, your values win over what Ideation would have derived from the structure. That is what lets you register a monomer whose structure carries no usable attachment-point labels; it also means an incorrect value registers an incorrect monomer, so state them only when you mean to.
Files written against the previous Ideation template keep working: the old spaced Natural Analog header is still accepted, CTAB still matches, and the now-obsolete Short Name column is simply ignored.
For SDF dataset imports you do not provide a monomer library. A V3000 SDF already embeds a monomer template for every monomer, and those templates are used to register any missing monomers on the Biotoolkit Monomer Service automatically — which is why the picker does not appear for SDF files.
Step 4: Configure peptide-specific options
Click Next. On the Properties Configuration step, a Peptide Specific Configuration section appears:
- HELM Column — the column that holds the HELM sequence notation (tabular imports only; auto-detected when named
HELM). - Reference Peptide — the peptide used by default as the basis for SAR slides created from this dataset. You can change it later per report.
Select and configure at least one main property, then submit.
Step 5: Watch the import
The final Import Status step shows the peptide import timeline:
Initializing → Registering Monomers → Parsing Peptide Sequences → Generating Alignment → Ready
- Registering Monomers runs when a monomer library was supplied, or when the dataset is a V3000 SDF (whose embedded monomer templates are registered on the Biotoolkit Monomer Service).
- Generating Alignment computes a position-by-position alignment from the dataset's own sequences, so the dataset arrives ready to build a SAR Slide from — no alignment file needed. It is saved as an alignment named Default alignment.
When the dataset reaches Ready, it opens on the dataset page.
Registration only adds monomers that are new to the Biotoolkit Monomer Service. Monomers whose symbol already exists there are used as-is and are never overwritten or updated — so a library or SDF cannot change a monomer that other datasets already rely on. The service also runs a duplication check on structure: if the same monomer is already registered under a different symbol, it is matched to that existing entry (as an alias) rather than registered again.
If it cannot run, the import still succeeds and the dataset simply has no default alignment. It is skipped for datasets with no HELM sequences and for datasets above 5,000 peptides. See How to Align Peptides.
If some peptides reference monomers that could not be resolved, they are imported with their HELM sequence preserved but without full structure or properties, and the dataset is flagged with an amber skipped-structures warning. See How to Resolve Missing Monomers.