AD
Data & Repro
Adaptyv
Adaptyv is a cloud laboratory platform that provides automated protein testing and validation services. Submit protein sequences via API or…
K-Dense-AI/claude-scientific-skillsView
Data & Repro
TP
tpd-ternary-complex-agent
Maintainer FreedomIntelligence · Last updated April 1, 2026
Targeted protein degradation ternary complex modeling and cooperativity prediction.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/tpd-ternary-complex-agent
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- The TPD Ternary Complex Agent specializes in predicting and modeling ternary complex formation for targeted protein degradation (TPD). It uses AlphaFold-Multimer, molecular dynamics, and deep learning to model Protein of Interest (POI)-degrader-E3 ligase assemblies, enabling rational optimization of PROTACs and molecular glues.
- When predicting ternary complex formation for degrader design.
- For understanding POI-E3 interface complementarity.
- To optimize linker geometry based on complex structure.
- When assessing ubiquitination site accessibility.
Source Doc
Excerpt From SKILL.md
Core Capabilities
-
Ternary Structure Prediction: Model full POI-degrader-E3 complexes.
-
Interface Analysis: Assess protein-protein interactions in complex.
-
Linker Geometry Optimization: Guide linker design from structures.
-
Ubiquitination Site Analysis: Identify accessible lysines for Ub transfer.
-
Cooperativity Scoring: Predict binding cooperativity (α factor).
-
E3 Comparison: Evaluate different E3 ligases for same target.
Supported E3 Ligases
| E3 Ligase | Structure | Complex Quality |
|---|---|---|
| CRBN-DDB1-CUL4A | High resolution | Excellent |
| VHL-ELOB-ELOC-CUL2 | High resolution | Excellent |
| MDM2 | Good | Good |
| IAP (cIAP1/XIAP) | Moderate | Moderate |
| DCAF15-DDB1 | Emerging | Developing |
| KEAP1 | High resolution | Good |
Workflow
-
Input: POI structure, degrader, E3 ligase specification.
-
Binary Modeling: Model POI-warhead and E3-ligand complexes.
-
Ternary Assembly: Predict full ternary complex structure.
-
MD Refinement: Molecular dynamics for complex stability.
-
Interface Scoring: Quantify POI-E3 interface quality.
-
Lysine Analysis: Map ubiquitination sites.
-
Output: Ternary structure, scores, optimization suggestions.
Use cases
- When predicting ternary complex formation for degrader design.
- For understanding POI-E3 interface complementarity.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- PROTAC_Design_Agent - Full PROTAC design
- Molecular_Glue_Discovery_Agent - Glue discovery
- Protein_Protein_Docking_Agent - PPI docking
- Molecular_Dynamics_Agent - MD simulations
Related skills
Related skills
AL
Data & Repro
alphafold
Validate protein designs using AlphaFold2 structure prediction. Use this skill when: (1) Validating designed sequences fold correctly, (2) P…
FreedomIntelligence/OpenClaw-Medical-SkillsView
AL
Data & Repro
AlphaFold DB
AlphaFold DB is a public repository of AI-predicted 3D protein structures for over 200 million proteins, maintained by DeepMind and EMBL-EBI…
K-Dense-AI/claude-scientific-skillsView
AN
Data & Repro
antibody-design-agent
Antibody design: epitope mapping, CDR engineering, bispecific construction.
FreedomIntelligence/OpenClaw-Medical-SkillsView