AD
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Adaptyv
Adaptyv is a cloud laboratory platform that provides automated protein testing and validation services. Submit protein s…
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数据与复现
DI
DiffDock
维护者 K-Dense Inc. · 最近更新 2026年4月1日
DiffDock is a diffusion-based deep learning tool for molecular docking that predicts 3D binding poses of small molecule ligands to protein targets. It represents the state-of-the-art in computational docking, crucial for structure-based drug discovery and chemical biology. **Core Capabilities:** - Predict ligand binding poses with high accuracy using deep learning - Support protein structures (PDB files) or sequence….
原始来源
K-Dense-AI/claude-scientific-skills
https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/diffdock
- 维护者
- K-Dense Inc.
- 许可
- MIT license
- 最近更新
- 2026年4月1日
技能摘要
来自 SKILL.md 的关键信息
核心说明
- 预测 ligand binding poses ，支持 high accuracy ，使用 深度学习。
- 支持 protein structures (PDB files) 或 sequences (，通过 ESMFold)。
- Process single complexes 或 batch virtual screening campaigns。
- 生成 confidence scores to assess prediction reliability。
- Handle diverse ligand inputs (SMILES，SDF，MOL2)。
原始文档
SKILL.md 摘录
When to Use This Skill
This skill should be used when:
- "Dock this ligand to a protein" or "predict binding pose"
- "Run molecular docking" or "perform protein-ligand docking"
- "Virtual screening" or "screen compound library"
- "Where does this molecule bind?" or "predict binding site"
- Structure-based drug design or lead optimization tasks
- Tasks involving PDB files + SMILES strings or ligand structures
- Batch docking of multiple protein-ligand pairs
Check Environment Status
Before proceeding with DiffDock tasks, verify the environment setup:
## Installation Options
**Option 1: Conda (Recommended)**
**Option 2: Docker**
**Important Notes:**
- GPU strongly recommended (10-100x speedup vs CPU)
- First run pre-computes SO(2)/SO(3) lookup tables (~2-5 minutes)
- Model checkpoints (~500MB) download automatically if not present
适用场景
- Dock this ligand to protein" 或 "predict binding pose。
- 运行 molecular docking" 或 "perform protein-ligand docking。
- Virtual screening" 或 "screen compound 库。
- Where does this molecule bind?" 或 "predict binding site。
不适用场景
- Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。
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