AL
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alphafold
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数据与复现
BI
bio-similarity-searching
维护者 FreedomIntelligence · 最近更新 2026年4月1日
Performs molecular similarity searches using Tanimoto coefficient on fingerprints via RDKit. Finds structurally similar compounds using ECFP or MACCS keys and clusters molecules by structural similarity using Butina clustering. Use when finding analogs of a query compound or clustering chemical libraries.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-similarity-searching
- 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
核心说明
- Python：DataStructs.TanimotoSimilarity()，Butina.ClusterData() (RDKit)。
- Find compounds similar to my query molecule" → Compute pairwise Tanimoto similarity on molecular fingerprints to rank 库 by structural resemblance to query，或 cluster compounds by chemical similarity ，使用 Butina 聚类. Python：DataStructs.TanimotoSimilarity()，Butina.ClusterData() (RDKit)。
- Find structurally similar molecules 、 cluster compound libraries。
- mol1 = Chem.MolFromSmiles('CCO') mol2 = Chem.MolFromSmiles('CCCO')。
- fp1 = AllChem.GetMorganFingerprintAsBitVect(mol1，radius=2，nBits=2048) fp2 = AllChem.GetMorganFingerprintAsBitVect(mol2，radius=2，nBits=2048)。
原始文档
SKILL.md 摘录
Tanimoto Similarity
from rdkit import Chem, DataStructs
from rdkit.Chem import AllChem
## Tanimoto similarity (0-1)
similarity = DataStructs.TanimotoSimilarity(fp1, fp2)
print(f'Tanimoto similarity: {similarity:.3f}')
Similarity Thresholds
| Threshold | Interpretation |
|---|---|
| > 0.85 | Very similar (likely same scaffold) |
| > 0.70 | Similar (likely related series) |
| > 0.50 | Moderate similarity |
| < 0.50 | Dissimilar |
适用场景
- 适合在finding analogs of query compound 或 聚类 chemical libraries时使用。
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
- molecular-descriptors - Generate fingerprints for similarity
- substructure-search - Pattern-based searching
- molecular-io - Load molecules for searching
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