PepSeA

PepSeA performs peptide sequence alignment and visualization to support structure–activity relationship (SAR) analysis of therapeutic peptides, including sequences that contain non‑natural amino acids.

Key Features:

• Multiple Sequence Alignment: Aligns peptide sequences that include non‑natural amino acids and supports linear, cyclic, and cross‑linked peptide architectures.
• HELM-based Visualization: Represents peptides using the Hierarchical Editing Language for Macromolecules (HELM) to visualize complex sequences and structural motifs.
• Structure–Activity Relationship Analysis: Facilitates SAR analysis by enabling detailed examination of peptide modifications and their effects on biological activity.

Scientific Applications:

• Lead optimization and design–make–test cycles: Supports lead optimization workflows in pharmaceutical peptide discovery and iterative design‑make‑test cycles.
• Targeting "undruggable" proteins: Enables exploration of peptides with non‑natural motifs to expand options for targeting proteins considered "undruggable".

Methodology:

Implements a stepwise approach to SAR analysis and has been applied to a ChEMBL peptide dataset.