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by-epitope-analysis

Identify and score epitope interface residues from co-crystal structures for binder design.

104|10|Updated Mar 23, 2026
Search Tags:#topology#hotspots#pdb#epitope#design-input#interface-analysis#biologics
One-click install
npx skills add https://github.com/001TMF/blatant-why --skill by-epitope-analysis
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: by-epitope-analysis
Source: https://github.com/001TMF/blatant-why/tree/main/templates/.claude/skills/by-epitope-analysis
Command: npx skills add https://github.com/001TMF/blatant-why --skill by-epitope-analysis

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires biopython, numpy, and includes scripts (resource) and references (resource) components.

What problem does it solve?

An automated workflow to identify and score epitope interface residues, generating hotspot lists and downstream-ready design inputs for PXDesign or BoltzGen from co-crystal structures.

Core Features & Use Cases

  • Detect interface residues across target and binder chains using dual distance cutoffs (4.0 A and 5.0 A) for robust hotspot identification.
  • Classify interface topology (pocket, groove, flat, linear) to guide appropriate design engines.
  • Compute and report druggability-inspired metrics and produce outputs like range_notation, boltzgen_binding, and pxdesign_hotspots for downstream tooling.
  • Use Case: Convert a co-crystal structure into a curated hotspot set to drive de novo binder design or antibody optimization.

Quick Start

Run the hotspot selection script on a downloaded co-crystal structure to generate hotspots.

Frequently Asked Questions about by-epitope-analysis

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I identify epitope hotspots from a PDB co-crystal structure for binder design?▼

Epitope interface residues are identified by calculating distances between target and binder chains in a co-crystal structure, selecting contacts within dual 4.0 Å and 5.0 Å cutoffs to robustly define hotspot residues.

What topology classifications are used for interface residues during epitope analysis?▼

During epitope analysis, interface topology is classified into pocket, groove, flat, or linear categories to help guide the selection of appropriate downstream design engines for your biologics workflow.

Can I use the hotspot outputs directly with PXDesign or BoltzGen workflows?▼

Yes, the analysis generates downstream-ready JSON artifacts containing formats like pxdesign_hotspots, boltzgen_binding, and range_notation, which are specifically designed to be passed directly into PXDesign or BoltzGen workflows.

Do I need multiple binder chains to calculate druggability metrics for an epitope?▼

You need one target chain and at least one binder chain in your co-crystal structure to calculate druggability-inspired metrics and accurately classify the interface topology for de novo binder design.

What outputs are generated when converting a co-crystal structure for de novo binder design?▼

Converting a co-crystal structure produces a JSON artifact containing druggability metrics, topology classification, range_notation, boltzgen_binding, and pxdesign_hotspots to drive downstream de novo binder design or antibody optimization.

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