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drug-bioactivity-assay

Official

Pull PubChem bioassays and active targets.

Education & Research#drug discovery#bioactivity#pubchem#assay retrieval#target proteins#activity outcome filtering#json data extraction
Authorlearningmatter-mit
Version1.0.0
Installs0

System Documentation

What problem does it solve?

Retrieve a chemical’s historical bioactivity evidence against biological targets and assay experiments from PubChem, focusing on which targets show an "Active" outcome.

Core Features & Use Cases

  • PubChem assay retrieval by compound ID (CID): Fetches assay summaries for a given molecule using the PubChem PUG REST assaysummary endpoint.
  • Active-only filtering: Optionally filters records to those whose "Activity Outcome" is "Active" to highlight likely binding/inhibition targets.
  • Actionable assay outputs: Produces JSON records containing assay identifiers (AID), target gene identifiers (Target GeneID when available), and activity values (e.g., Activity Value [uM]) for downstream promiscuity or specificity analysis.
  • Use case: For a candidate drug (e.g., Imatinib), extract all assay evidence, filter to actives, and analyze the breadth of target engagement by gene and activity potency.

Quick Start

Use the command to fetch active PubChem assay records for Imatinib (CID 5291) into a JSON file for downstream target analysis.

Dependency Matrix

Required Modules

None required

Components

scripts

💻 Claude Code Installation

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Please help me install this Skill:
Name: drug-bioactivity-assay
Download link: https://github.com/learningmatter-mit/AtomisticSkills/archive/main.zip#drug-bioactivity-assay

Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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