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SMILES Profiling

该 Skill 接收单个 SMILES 字符串，依次调用 SwissTargetPrediction、PubChem、ADMETlab 3.0、ChEMBL 和 PK-Smart，抽取预测靶点、身份与理化性质、ADMET 与成药性、相似化合物与作用机制、药代参数，合并为一份简短报告；可归一化盐/反离子，并在个别来源不可用时降级继续。

hendr15k
hendr15k
热度 41.68
最近更新 2026-05-11 17:41:40
分类：数据依赖：代码执行 / 读写文件 / 第三方 API应用场景：研究 / 报告撰写 / 数据处理 / API 集成 ...

安装技能

复制下面的话术发给你的 Agent，它会通过 secure-skills 检索并安装该技能。

执行命令安装此 skill： npx secure-skills-cli add smiles-profiling
Metadata
name
smiles-profiling
description
Comprehensive SMILES profiling through SwissTargetPrediction, PubChem, ADMETlab 3.0, ChEMBL, and PK-Smart. Use when given a single SMILES to extract predicted targets, exact identity and physicochemical baselines, known analogs and mechanisms, ADMET properties, and pharmacokinetic estimates; handles salts/counterions and degrades gracefully when any source is unavailable.

SMILES Profiling

Turn one SMILES into a compact pharmacology profile.

Tool stack

Tool Use
SwissTargetPrediction Predicted protein targets with probabilities
PubChem Exact CID, synonyms, MW, XLogP, TPSA, HBD/HBA, rotatable bonds
ADMETlab 3.0 ADMET flags, drug-likeness, toxicity sections
ChEMBL Similarity hits, max phase, known mechanisms, target names
PK-Smart Human and animal PK estimates (VDss, CL, t½, fu, MRT)

Workflow

  1. Use the user-provided SMILES as-is unless it clearly needs cleanup.
  2. Normalize only obvious salts/counterions.
  3. Run SwissTargetPrediction for target hypotheses.
  4. Run PubChem for identity and physicochemical baseline.
  5. Run ADMETlab 3.0 for ADMET flags and drug-likeness.
  6. Run ChEMBL for similarity hits and mechanism context.
  7. Run PK-Smart last for PK estimates.
  8. Merge the outputs into one short report, preferring direct database evidence over predictions.

Preferred scripts

  • scripts/run_smiles_profile.py <SMILES> for the full report.
  • scripts/run_smiles_smoke.py --cases <tsv> for regression/benchmark runs.

Extraction notes

  • SwissTargetPrediction: capture the top 5 targets, probabilities, and species.
  • PubChem: capture CID, IUPAC name, synonyms, MW, XLogP, TPSA, HBD/HBA, and rotatable bonds.
  • ADMETlab 3.0: capture the section list and any obvious toxicity/drug-likeness flags.
  • ChEMBL: capture the similarity threshold, top hits, max phase, mechanism_of_action, and target name.
  • PK-Smart: capture VDss, CL, t½, fu, MRT, and animal PK when available.

Handling edge cases

  • Salts/mixtures: strip common counterions first.
  • Invalid SMILES: fail cleanly, do not crash.
  • Missing tools: continue with the remaining sources.
  • PubChem miss: report the miss and continue.
  • ChEMBL miss: automatically fall back from 90 → 80 → 70 similarity.

Output shape

SMILES: CC(=O)OC1=CC=CC=C1C(=O)O

## SwissTargetPrediction
- Top target: PTGS1 (prob: 0.76)

## PubChem
- CID: 2244 | Name: 2-acetyloxybenzoic acid
- MW: 180.16 Da | XLogP: 1.2 | TPSA: 63.6 Ų

## ADMETlab 3.0
- MW: 180.04 Da | QED: N/A

## ChEMBL
- Top hit: CHEMBL25 ASPIRIN | sim 100 | phase 4
- Mechanism: Cyclooxygenase inhibitor -> Cyclooxygenase

## PK-Smart
- VDss: 0.23 L/kg | CL: 10.41 mL/min/kg
- t½: 0.34 hr | fu: 0.67