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

• 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" }

Exit codes:

• 0

• Success

• 1

• 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.