protac-degraders

Design PROTAC degraders with E3 ligase choice and linker design.

6|2|Updated Jun 11, 2026

Search Tags:#bioinformatics #PROTAC #degrader design #E3 ligase #linker design #ternary complex #degradation efficiency

Ready to run

npx skills add https://github.com/pradyumnasagar/open-research-skills --skill protac-degraders

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: protac-degraders
Source: https://github.com/pradyumnasagar/open-research-skills/tree/main/skills/chemoinformatics/protac-degraders
Command: npx skills add https://github.com/pradyumnasagar/open-research-skills --skill protac-degraders

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires RDKit, OpenMM, PRosettaC, DeepTernary, AlphaFold3, Boltz-1, Boltz-2, and includes scripts (resource) and references (resource) and assets (resource) components.

What problem does it solve?

This Skill addresses the complex task of designing and analyzing PROTAC degraders, providing a comprehensive framework for molecular glue and bivalent degrader design.

Core Features & Use Cases

PROTAC Design: Designs PROTACs with explicit E3 ligase choice, linker design, and ternary complex prediction.
Linker Design Principles: Offers guidelines for linker length, rigidity, chemistry, and compatibility.
Ternary Complex Prediction: Utilizes PRosettaC, DeepTernary, AlphaFold3, and Boltz-1/2 for accurate predictions.
Cooperativity Analysis: Measures the binding strength of PROTACs and provides insights for optimization.
DC50 / Dmax Characterization: Assesses degradation efficiency and potential hook effects.
PROTAC Databases: Accesses and utilizes publicly available PROTAC databases for reference.
Per-Tool Failure Modes: Identifies and mitigates common pitfalls in PROTAC design and analysis.
Use Case: A researcher designing a PROTAC degrader for a specific target protein can use this Skill to predict the ternary complex stability and optimize the linker design.

Quick Start

Use the protac-degraders skill to design a PROTAC degrader for a target protein using the CRBN E3 ligase and a PEG linker.

Frequently Asked Questions about protac-degraders

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

FAQPage Schema

How do I predict ternary complex stability for PROTAC degraders?▼

Predict ternary complex stability for PROTAC degraders using integrated tools like PRosettaC, DeepTernary, AlphaFold3, and Boltz-1/2. These models calculate structural configurations and cooperativity to help you assess and optimize degradation efficiency.

How do I optimize linker design for PROTACs?▼

Design PROTAC linkers by applying principles for optimal length, rigidity, and chemical compatibility. This Skill evaluates linker chemistry to ensure proper ternary complex formation, balancing flexibility and stability to maximize target protein degradation.

How is DC50 and Dmax characterized in PROTAC degradation efficiency?▼

Characterize DC50 and Dmax to assess PROTAC degradation efficiency and identify potential hook effects. This analysis measures the concentration-dependent degradation profile to determine the optimal therapeutic window for your bivalent degrader.

How do I choose an E3 ligase for PROTAC design?▼

Choose an E3 ligase like CRBN for PROTAC design based on target protein accessibility and binding cooperativity. This Skill provides a framework to evaluate different E3 ligases and their impact on ternary complex stability and degradation success.

Do I need RDKit and OpenMM to analyze PROTAC degraders?▼

You need RDKit and OpenMM installed to analyze PROTAC degraders, as this Skill relies on them for cheminformatics processing and molecular dynamics simulations. Various machine learning models are also required for full computational analysis.

What are common failure modes in PROTAC ternary complex prediction?▼

Mitigate common PROTAC design failures by identifying per-tool failure modes and utilizing publicly available PROTAC databases for reference. This approach helps anticipate structural prediction errors and optimize ternary complex cooperativity.