RCSB PDB MCP Server for Claude Code 2 tools — connect in under 2 minutes
Claude Code is Anthropic's agentic CLI for terminal-first development. Add RCSB PDB as an MCP server in one command and Claude Code will discover every tool at runtime — ideal for automation pipelines, CI/CD integration, and headless workflows via the Vinkius.
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Vinkius supports streamable HTTP and SSE.
Vinkius Desktop App
The modern way to manage MCP Servers — no config files, no terminal commands. Install RCSB PDB and 2,500+ MCP Servers from a single visual interface.
# Your Vinkius token — get it at cloud.vinkius.com
claude mcp add rcsb-pdb --transport http "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
* 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.
Claude Code registers RCSB PDB as an MCP server in a single terminal command. Once connected, Claude Code discovers all 2 tools at runtime and can call them headlessly — ideal for CI/CD pipelines, cron jobs, and automated workflows where RCSB PDB data drives decisions without human intervention.
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 Claude Code 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 Claude Code via MCP
Follow these steps to integrate the RCSB PDB MCP Server with Claude Code.
Install Claude Code
Run npm install -g @anthropic-ai/claude-code if not already installed
Add the MCP Server
Run the command above in your terminal
Verify the connection
Run claude mcp to list connected servers, or type /mcp inside a session
Start using RCSB PDB
Ask Claude: "Using RCSB PDB, show me..." — 2 tools are ready
Why Use Claude Code with the RCSB PDB MCP Server
Claude Code provides unique advantages when paired with RCSB PDB through the Model Context Protocol.
Single-command setup: `claude mcp add` registers the server instantly — no config files to edit or applications to restart
Terminal-native workflow means MCP tools integrate seamlessly into shell scripts, CI/CD pipelines, and automated DevOps tasks
Claude Code runs headlessly, enabling unattended batch processing using RCSB PDB tools in cron jobs or deployment scripts
Built by the same team that created the MCP protocol, ensuring first-class compatibility and the fastest adoption of new protocol features
RCSB PDB + Claude Code Use Cases
Practical scenarios where Claude Code combined with the RCSB PDB MCP Server delivers measurable value.
CI/CD integration: embed RCSB PDB tool calls in your deployment pipeline to validate configurations or fetch secrets before shipping
Headless batch processing: schedule Claude Code to query RCSB PDB nightly and generate reports without human intervention
Shell scripting: pipe RCSB PDB outputs into other CLI tools for data transformation, filtering, and aggregation
Infrastructure monitoring: run Claude Code in a cron job to query RCSB PDB status endpoints and alert on anomalies
RCSB PDB MCP Tools for Claude Code (2)
These 2 tools become available when you connect RCSB PDB to Claude Code 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 Claude Code
Ready-to-use prompts you can give your Claude Code 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 Claude Code
Common issues when connecting RCSB PDB to Claude Code through the Vinkius, and how to resolve them.
Command not found: claude
npm install -g @anthropic-ai/claude-codeConnection timeout
RCSB PDB + Claude Code FAQ
Common questions about integrating RCSB PDB MCP Server with Claude Code.
How do I add an MCP server to Claude Code?
claude mcp add --transport http "" in your terminal. Claude Code registers the server and discovers all tools immediately.Can Claude Code run MCP tools in headless mode?
How do I list all connected MCP servers?
claude mcp in your terminal to see all registered servers and their status, or type /mcp inside an active Claude Code session.Connect RCSB PDB with your favorite client
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Connect RCSB PDB to Claude Code
Get your token, paste the configuration, and start using 2 tools in under 2 minutes. No API key management needed.