chembl-search

ChEMBL Search

Search the complete ChEMBL database of bioactive molecules, drug targets, and binding data using natural language queries powered by Valyu's semantic search API.

Why This Skill is Powerful

• No API Parameter Parsing: Just pass natural language queries directly - no need to construct complex search parameters
• Semantic Search: Understands the meaning of your query, not just keyword matching
• Full-Text Access: Returns complete compound and target information
• Image Links: Includes molecular structures and data visualizations
• Comprehensive Coverage: Access to all ChEMBL bioactive molecule data for drug discovery

Requirements

1. Node.js 18+ (uses built-in fetch)
2. Valyu API key from https://platform.valyu.ai ($10 free credits)

CRITICAL: Script Path Resolution

The scripts/search commands in this documentation are relative to this skill's installation directory.

Before running any command, locate the script using:

CHEMBL_SCRIPT=$(find ~/.claude/plugins/cache -name "search" -path "*/chembl-search/*/scripts/*" -type f 2>/dev/null | head -1)

Then use the full path for all commands:

$CHEMBL_SCRIPT "kinase inhibitors" 15

API Key Setup Flow

When you run a search and receive "setup_required": true, follow this flow:

1. Ask the user for their API key: "To search ChEMBL, I need your Valyu API key. Get one free ($10 credits) at https://platform.valyu.ai"

2. Once the user provides the key, run:

   scripts/search setup <api-key>
   

3. Retry the original search.

When to Use This Skill

• Finding bioactive compounds for drug discovery
• Target-based compound searching
• Compound property optimization
• Assay data and biological activity research
• Structure-activity relationship studies
• Lead compound identification

Output Format

{
  "success": true,
  "type": "chembl_search",
  "query": "kinase inhibitors",
  "result_count": 10,
  "results": [
    {
      "title": "Compound/Assay Title",
      "url": "https://chembl.org/...",
      "content": "Compound data, targets, assay results...",
      "source": "chembl",
      "relevance_score": 0.95,
      "images": ["https://example.com/structure.png"]
    }
  ],
  "cost": 0.025
}