Ideation's Peptide feature brings structure-activity relationship (SAR) analysis to peptides: import peptide datasets (HELM or SDF), build interactive SAR Reports around a reference peptide, and explore hotspots, multi-position synergies, and structural clusters across your series.
The Peptide feature is under active development and we are releasing it early so you can start working with it and help shape it. Please don't hesitate to share feedback, report bugs or issues, and suggest or discuss new features with us. Your input directly drives what we build next.
What's in this documentation
The Peptides documentation is organized into three kinds of pages:
Tutorial — a guided, end-to-end walkthrough:
- Getting Started with Peptides — import a dataset, resolve a missing monomer, create a SAR Report, and take a first look at the viewer.
How-To guides — focused, task-oriented instructions:
- How to Create a Peptide Dataset
- How to Resolve Missing Monomers
- How to Create a Peptide SAR Report
- How to Align Peptides
- How to Explore the Peptide Viewer
- How to Analyze Hotspots and Synergies
- How to Cluster Peptides
Explanation — the concepts behind the feature:
- Understanding Peptides in Ideation — SAR Report vs SAR Slide, HELM and monomers, the Biotoolkit Monomer Service, and what each analysis tells you.
- Understanding Peptide Alignment — the method behind the alignments Ideation computes for you.
- Understanding Hotspots and Synergies — how impact and interaction scores are computed, and how to avoid over-reading them.
- Understanding Peptide Clustering — how peptides are grouped, what the quality figures mean, and what the scatter plot does and doesn't show.
Release notes — what changed, release by release:
- Peptides Release Notes — the features and fixes in each early-access release.
How to start
- Check access. The Peptide dataset type and peptide SAR Reports require the peptide plugin to be enabled for your organization. If you don't see the Peptide option, contact your administrator.
- Follow the tutorial. Work through Getting Started with Peptides end to end — it links out to the detailed how-to guides as you go.
- Go deeper. Once you have a report open, use the how-to guides for the viewer, hotspot/synergy analysis, and clustering, and read Understanding Peptides for the concepts.