Summary This source did not publish a separate summary. Review SKILL.md before using the skill.
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 parametersSemantic Search : Understands the meaning of your query, not just keyword matchingFull-Text Access : Returns complete compound and target informationImage Links : Includes molecular structures and data visualizationsComprehensive Coverage : Access to all ChEMBL bioactive molecule data for drug discovery
Requirements
Node.js 18+ (uses built-in fetch)
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:
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 "
Once the user provides the key, run:
scripts/search setup <api-key>
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
}
Processing Results
With jq # Get compound titles
scripts/search "query" 10 | jq -r '.results[].title'
# Get URLs
scripts/search "query" 10 | jq -r '.results[].url'
# Extract full content
scripts/search "query" 10 | jq -r '.results[].content'
Common Use Cases
Drug Discovery # Find lead compounds
scripts/search "JAK2 selective inhibitors for myelofibrosis" 50
Target Validation # Search for target information
scripts/search "protein kinase B binding assays" 20
SAR Analysis # Find structure-activity relationships
scripts/search "benzimidazole derivatives anticancer activity" 15
Mechanism Research # Search for mechanism data
scripts/search "allosteric modulators of NMDA receptors" 25
Error Handling All commands return JSON with success field:
{
"success": false,
"error": "Error message"
}
0 - Success1 - Error (check JSON for details)
API Endpoint
Base URL: https://api.valyu.ai/v1
Endpoint: /search
Authentication: X-API-Key header
Architecture scripts/
├── search # Bash wrapper
└── search.mjs # Node.js CLI
Direct API calls using Node.js built-in fetch(), zero external dependencies.
Adding to Your Project If you're building an AI project and want to integrate ChEMBL Search directly into your application, use the Valyu SDK:
Python Integration from valyu import Valyu
client = Valyu(api_key="your-api-key")
response = client.search(
query="your search query here",
included_sources=["valyu/valyu-chembl"],
max_results=20
)
for result in response["results"]:
print(f"Title: {result['title']}")
print(f"URL: {result['url']}")
print(f"Content: {result['content'][:500]}...")
TypeScript Integration import { Valyu } from "valyu-js";
const client = new Valyu("your-api-key");
const response = await client.search({
query: "your search query here",
includedSources: ["valyu/valyu-chembl"],
maxResults: 20
});
response.results.forEach((result) => {
console.log(`Title: ${result.title}`);
console.log(`URL: ${result.url}`);
console.log(`Content: ${result.content.substring(0, 500)}...`);
});
See the Valyu docs for full integration examples and SDK reference.
