protac-degraders

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.