RCSB PDB MCP Server for LlamaIndex 2 tools — connect in under 2 minutes
LlamaIndex specializes in data-aware AI agents that connect LLMs to structured and unstructured sources. Add RCSB PDB as an MCP tool provider through Vinkius and your agents can query, analyze, and act on live data alongside your existing indexes.
ASK AI ABOUT THIS MCP SERVER
Vinkius supports streamable HTTP and SSE.
import asyncio
from llama_index.tools.mcp import BasicMCPClient, McpToolSpec
from llama_index.core.agent.workflow import FunctionAgent
from llama_index.llms.openai import OpenAI
async def main():
# Your Vinkius token. get it at cloud.vinkius.com
mcp_client = BasicMCPClient("https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp")
mcp_tool_spec = McpToolSpec(client=mcp_client)
tools = await mcp_tool_spec.to_tool_list_async()
agent = FunctionAgent(
tools=tools,
llm=OpenAI(model="gpt-4o"),
system_prompt=(
"You are an assistant with access to RCSB PDB. "
"You have 2 tools available."
),
)
response = await agent.run(
"What tools are available in RCSB PDB?"
)
print(response)
asyncio.run(main())
* Every MCP server runs on Vinkius-managed infrastructure inside AWS - a purpose-built runtime with per-request V8 isolates, Ed25519 signed audit chains, and sub-40ms cold starts optimized for native MCP execution. See our infrastructure
About RCSB PDB MCP Server
Connect your AI agent to the RCSB Protein Data Bank — the world's repository of experimentally determined 3D structural data for biological macromolecules.
LlamaIndex agents combine RCSB PDB tool responses with indexed documents for comprehensive, grounded answers. Connect 2 tools through Vinkius and query live data alongside vector stores and SQL databases in a single turn. ideal for hybrid search, data enrichment, and analytical workflows.
What you can do
- Structure Search — Find protein, DNA, and RNA structures by name, function, disease association, or organism across 220K+ experimentally determined entries
- PDB Entry Lookup — Get complete structural details by 4-character PDB ID (e.g., 1HHO for hemoglobin, 6LU7 for SARS-CoV-2 main protease) including experimental method, resolution, and bound molecules
The RCSB PDB MCP Server exposes 2 tools through the Vinkius. Connect it to LlamaIndex in under two minutes — no API keys to rotate, no infrastructure to provision, no vendor lock-in. Your configuration, your data, your control.
How to Connect RCSB PDB to LlamaIndex via MCP
Follow these steps to integrate the RCSB PDB MCP Server with LlamaIndex.
Install dependencies
Run pip install llama-index-tools-mcp llama-index-llms-openai
Replace the token
Replace [YOUR_TOKEN_HERE] with your Vinkius token
Run the agent
Save to agent.py and run: python agent.py
Explore tools
The agent discovers 2 tools from RCSB PDB
Why Use LlamaIndex with the RCSB PDB MCP Server
LlamaIndex provides unique advantages when paired with RCSB PDB through the Model Context Protocol.
Data-first architecture: LlamaIndex agents combine RCSB PDB tool responses with indexed documents for comprehensive, grounded answers
Query pipeline framework lets you chain RCSB PDB tool calls with transformations, filters, and re-rankers in a typed pipeline
Multi-source reasoning: agents can query RCSB PDB, a vector store, and a SQL database in a single turn and synthesize results
Observability integrations show exactly what RCSB PDB tools were called, what data was returned, and how it influenced the final answer
RCSB PDB + LlamaIndex Use Cases
Practical scenarios where LlamaIndex combined with the RCSB PDB MCP Server delivers measurable value.
Hybrid search: combine RCSB PDB real-time data with embedded document indexes for answers that are both current and comprehensive
Data enrichment: query RCSB PDB to augment indexed data with live information before generating user-facing responses
Knowledge base agents: build agents that maintain and update knowledge bases by periodically querying RCSB PDB for fresh data
Analytical workflows: chain RCSB PDB queries with LlamaIndex's data connectors to build multi-source analytical reports
RCSB PDB MCP Tools for LlamaIndex (2)
These 2 tools become available when you connect RCSB PDB to LlamaIndex via MCP:
get_pdb_structure
PDB IDs are 4-character codes like 1HHO, 6LU7, 7BNN. Get full structural details by PDB ID
search_pdb
Returns PDB ID, title, experimental method (X-ray, Cryo-EM, NMR), resolution, authors, and bound ligands. Essential for drug discovery and structural biology. Search 220K+ 3D molecular structures in the Protein Data Bank
Example Prompts for RCSB PDB in LlamaIndex
Ready-to-use prompts you can give your LlamaIndex agent to start working with RCSB PDB immediately.
"Show me the structure of the SARS-CoV-2 main protease."
"Get full structural details for PDB entry 1HHO — what protein is it?"
"Find all cryo-EM structures of ribosome complexes."
Troubleshooting RCSB PDB MCP Server with LlamaIndex
Common issues when connecting RCSB PDB to LlamaIndex through the Vinkius, and how to resolve them.
BasicMCPClient not found
pip install llama-index-tools-mcpRCSB PDB + LlamaIndex FAQ
Common questions about integrating RCSB PDB MCP Server with LlamaIndex.
How does LlamaIndex connect to MCP servers?
Can I combine MCP tools with vector stores?
Does LlamaIndex support async MCP calls?
Connect RCSB PDB with your favorite client
Step-by-step setup guides for every MCP-compatible client and framework:
Anthropic's native desktop app for Claude with built-in MCP support.
AI-first code editor with integrated LLM-powered coding assistance.
GitHub Copilot in VS Code with Agent mode and MCP support.
Purpose-built IDE for agentic AI coding workflows.
Autonomous AI coding agent that runs inside VS Code.
Anthropic's agentic CLI for terminal-first development.
Python SDK for building production-grade OpenAI agent workflows.
Google's framework for building production AI agents.
Type-safe agent development for Python with first-class MCP support.
TypeScript toolkit for building AI-powered web applications.
TypeScript-native agent framework for modern web stacks.
Python framework for orchestrating collaborative AI agent crews.
Leading Python framework for composable LLM applications.
Data-aware AI agent framework for structured and unstructured sources.
Microsoft's framework for multi-agent collaborative conversations.
Connect RCSB PDB to LlamaIndex
Get your token, paste the configuration, and start using 2 tools in under 2 minutes. No API key management needed.