--- title: "Getting Started with Peptides" slug: "tutorial-getting-started-with-peptides" status: "update" updated: 2026-10-14T09:21:17Z published: 2026-10-14T09:21:17Z canonical: "docs.discngine.com/tutorial-getting-started-with-peptides" --- > ## Documentation Index > Fetch the complete documentation index at: https://docs.discngine.com/llms.txt > Use this file to discover all available pages before exploring further. # Getting Started with Peptides This tutorial walks you end to end: import a peptide dataset, resolve a missing monomer, create a peptide SAR Report, and take a first look at the viewer. It ties together the individual how-to guides into one journey. ## Prerequisites - You are logged into Ideation, and the peptide plugin is enabled. - You have a peptide file with a HELM column (CSV/Excel) or a V3000 SDF. If you use custom monomers, have a monomer library file ready (or plan to register them in the Biotoolkit Monomer Service). ## Step 1: Import a peptide dataset 1. On the **Home** page, click **Create Dataset**. 2. Choose a **Project** and drop your file. Ideation detects a peptide file and sets **Dataset Type** to **Peptide**; check it, and select it yourself for a compressed file. 3. If your file uses custom monomers, add a **Monomer Library File**. 4. Click **Next**, confirm the **HELM Column** and a **Reference Peptide** under **Peptide Specific Configuration**, select at least one property, and submit. 5. Watch the import timeline: **Initializing → Registering Monomers → Parsing Peptide Sequences → Ready**. ![The Import Status step showing the four-stage peptide import timeline](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Documentation/import-status-timeline-peptide.png?sv=2026-02-06&spr=https&st=2026-10-27T11%3A59%3A05Z&se=2026-10-27T12%3A59%3A05Z&sr=c&sp=r&sig=SmGsIjtdSkrKCjrdusIENwz8cx18IRPtJTkjDiJTTNk%3D) Once the dataset is ready, Ideation computes two alignments for it in the background — a **Center-star alignment** and a **PepSeA alignment** — so you don't need to bring one. For the full details, see [How to Create a Peptide Dataset](/public/docs/how-to-create-peptide-dataset). ## Step 2: Resolve any missing monomers If some peptides used monomers Ideation could not resolve, the dataset opens with an **amber warning triangle** in the title bar (*"N structures imported with missing data"*) and a **Missing Monomers** column in the grid, with the affected rows highlighted. 1. Click the warning to open the import issues dialog and read why each structure is listed and what it is missing — a missing monomer is fixable here, a HELM error has to be corrected in the source file (see [HELM Rules for Peptide Import](/public/docs/reference-helm-rules)). 2. If the dialog ends with a box listing monomers missing from the Biotoolkit Monomer Service, open the **Biotoolkit Monomer Service App** and register them. 3. Back in the dialog, click **Sync monomers** to recompute structures and properties. ![The dataset page with the amber import issues warning, the Missing Monomers column, and highlighted rows](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Documentation/dataset-missing-monomers.png?sv=2026-02-06&spr=https&st=2026-10-27T11%3A59%3A05Z&se=2026-10-27T12%3A59%3A05Z&sr=c&sp=r&sig=SmGsIjtdSkrKCjrdusIENwz8cx18IRPtJTkjDiJTTNk%3D) See [How to Resolve Missing Monomers](/public/docs/how-to-resolve-missing-monomers) for more. ## Step 3: Create a SAR Report 1. From **Home**, click **Create SAR Report** and pick your peptide dataset. 2. Choose a **Reference Peptide**. 3. Under **Alignment**, keep the alignment that is preselected — one of the two that came with the import, badged **Center-star** or **PepSeA**. If they still read **In progress**, wait a moment for one to complete. To use your own instead, click **New Alignment → Import from a file**. 4. Click **Generate SAR Slide**. ![The Create New SAR Report dialog showing the reference peptide and the Alignment section with its Available Alignments list](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Documentation/create-sar-report-peptide.png?sv=2026-02-06&spr=https&st=2026-10-27T11%3A59%3A05Z&se=2026-10-27T12%3A59%3A05Z&sr=c&sp=r&sig=SmGsIjtdSkrKCjrdusIENwz8cx18IRPtJTkjDiJTTNk%3D) Your report opens with its first **SAR Slide**. You can add more slides later with **Add SAR Slide**. See [How to Create a Peptide SAR Report](/public/docs/how-to-create-peptide-sar-report) and [How to Align Peptides](/public/docs/how-to-align-peptides). ## Step 4: Take a first look at the viewer The viewer draws your reference peptide's backbone, with its bridges, branches, chemical objects, and regions. Try these first actions: - **Pan and zoom** the canvas in **Pan & Drag** mode. - **Click a monomer** to open its gallery of variants and endpoint values. - Switch to **Select** mode to select a run of monomers and **Create Region**. ![The peptide viewer with the backbone, a cyclized bridge, regions, and open galleries](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Documentation/viewer-glucagon-overview.png?sv=2026-02-06&spr=https&st=2026-10-27T11%3A59%3A05Z&se=2026-10-27T12%3A59%3A05Z&sr=c&sp=r&sig=SmGsIjtdSkrKCjrdusIENwz8cx18IRPtJTkjDiJTTNk%3D) ## What you learned - A **peptide dataset** is imported from a HELM file or SDF, with an optional **monomer library**; unknown monomers are registered via the **Biotoolkit Monomer Service**. - Missing monomers are resolved by registering them and then **syncing** the dataset. - Import also **computes an alignment** for you, so a dataset is ready to analyze straight away; you can still import or regenerate one at any time. - A **SAR Report** holds one or more **SAR Slides**, each built on a **reference peptide** and an **alignment**. - The viewer visualizes the backbone, branches, bridges, cyclization, regions, and per-position variants. ## Next steps - [How to Align Peptides](/public/docs/how-to-align-peptides) - [How to Explore the Peptide Viewer](/public/docs/how-to-explore-peptide-viewer) - [How to Analyze Hotspots and Synergies](/public/docs/how-to-analyze-hotspots-and-synergies) - [How to Cluster Peptides](/public/docs/how-to-cluster-peptides) - [Understanding Peptides in Ideation](/public/docs/explanation-understanding-peptides)