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tpd-ternary-complex-agent

维护者 FreedomIntelligence · 最近更新 2026年4月1日

Targeted protein degradation ternary complex modeling and cooperativity prediction.

OpenClawNanoClaw分析处理复现实验tpd-ternary-complex-agent🧠 bioos extended suitedrug discovery & designtargeted

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/tpd-ternary-complex-agent

维护者
FreedomIntelligence
许可
MIT
最近更新
2026年4月1日

技能摘要

来自 SKILL.md 的关键信息

2 min

核心说明

  • TPD Ternary Complex Agent specializes in predicting 、 modeling ternary complex formation ，用于 targeted protein degradation (TPD). It uses AlphaFold-Multimer，molecular dynamics，、 深度学习 to model Protein of Interest (POI)-degrader-E3 ligase assemblies，enabling rational optimization of PROTACs 、 molecular glues。
  • When predicting ternary complex formation ，用于 degrader design。
  • 用于 understanding POI-E3 interface complementarity。
  • To optimize linker geometry based on complex structure。
  • When assessing ubiquitination site accessibility。

原始文档

SKILL.md 摘录

Core Capabilities

  1. Ternary Structure Prediction: Model full POI-degrader-E3 complexes.

  2. Interface Analysis: Assess protein-protein interactions in complex.

  3. Linker Geometry Optimization: Guide linker design from structures.

  4. Ubiquitination Site Analysis: Identify accessible lysines for Ub transfer.

  5. Cooperativity Scoring: Predict binding cooperativity (α factor).

  6. E3 Comparison: Evaluate different E3 ligases for same target.

Supported E3 Ligases

E3 LigaseStructureComplex Quality
CRBN-DDB1-CUL4AHigh resolutionExcellent
VHL-ELOB-ELOC-CUL2High resolutionExcellent
MDM2GoodGood
IAP (cIAP1/XIAP)ModerateModerate
DCAF15-DDB1EmergingDeveloping
KEAP1High resolutionGood

Workflow

  1. Input: POI structure, degrader, E3 ligase specification.

  2. Binary Modeling: Model POI-warhead and E3-ligand complexes.

  3. Ternary Assembly: Predict full ternary complex structure.

  4. MD Refinement: Molecular dynamics for complex stability.

  5. Interface Scoring: Quantify POI-E3 interface quality.

  6. Lysine Analysis: Map ubiquitination sites.

  7. Output: Ternary structure, scores, optimization suggestions.

适用场景

  • When predicting ternary complex formation ，用于 degrader design。
  • 用于 understanding POI-E3 interface complementarity。

不适用场景

  • Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。

上游相关技能

  • PROTAC_Design_Agent - Full PROTAC design
  • Molecular_Glue_Discovery_Agent - Glue discovery
  • Protein_Protein_Docking_Agent - PPI docking
  • Molecular_Dynamics_Agent - MD simulations

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