EBI PDBe MCP Server for Claude CodeGive Claude Code instant access to 16 tools to Get Assemblies, Get Binding Sites, Get Cofactors, and more
GDPR Free for SubscribersClaude Code is Anthropic's agentic CLI for terminal-first development. Add EBI PDBe 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 Vinkius.
Ask AI about this MCP Server for Claude Code
The EBI PDBe MCP Server for Claude Code is a standout in the The Unthinkable category — giving your AI agent 16 tools to work with, ready to go from day one.
Vinkius delivers Streamable HTTP and SSE to any MCP client
Gemini# Your Vinkius token. get it at cloud.vinkius.com
claude mcp add ebi-pdbe --transport http "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"Vinkius Desktop App
The modern way to manage MCP Servers — no config files, no terminal commands. Install EBI PDBe and 4,000+ MCP Servers from a single visual interface.
* 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 EBI PDBe MCP Server
Connect to the PDBe (Protein Data Bank in Europe) API and access the world's most comprehensive repository of experimentally determined 3D macromolecular structures.
Claude Code registers EBI PDBe as an MCP server in a single terminal command. Once connected, Claude Code discovers all 16 tools at runtime and can call them headlessly. ideal for CI/CD pipelines, cron jobs, and automated workflows where EBI PDBe data drives decisions without human intervention.
What you can do
- Structure Summaries — Get titles, authors, deposition dates, resolution, and experimental methods for any PDB entry
- Molecular Entities — Retrieve protein chains, nucleic acids, ligands, their sequences, source organisms, and gene names
- Binding Sites & Ligands — Access ligand binding pocket residues, small molecule ligands with formulas and weights
- Quality Assessment — Check resolution, R-factors, and overall quality scores for structure reliability
- UniProt Mappings — Map between UniProt sequence positions and PDB residue numbers
- Biological Assemblies — Understand quaternary structure — monomer, dimer, tetramer, or higher-order complexes
- Structure Search — Full-text Solr search across 200+ PDB metadata fields
- Publications — Find primary citations, PubMed IDs, and related structural studies
The EBI PDBe MCP Server exposes 16 tools through the Vinkius. Connect it to Claude Code in under two minutes — credentials fully managed, no infrastructure to provision, no vendor lock-in. Your configuration, your data, your control.
All 16 EBI PDBe tools available for Claude Code
When Claude Code connects to EBI PDBe through Vinkius, your AI agent gets direct access to every tool listed below — spanning pdb, protein-structure, 3d-structures, and more. Every call runs in a secure, isolated environment with full audit visibility. Beyond a simple connection, you get real-time monitoring of agent activity, enterprise governance, and optimized token usage.
Get assemblies on EBI PDBe
Returns assembly IDs, composition (which entities and how many copies), preferred assembly flag, and form description. Critical for understanding whether a protein functions as a monomer, dimer, tetramer, or higher-order complex. Get biological assembly information (quaternary structure)
Get binding sites on EBI PDBe
Critical for drug discovery, molecular docking, and understanding protein-ligand interactions. Get ligand binding site residues and interactions
Get cofactors on EBI PDBe
Cofactors like heme, NAD+, FAD, and metal ions are essential for enzyme catalysis and protein function. Get cofactor and prosthetic group annotations
Get experiment on EBI PDBe
Get experimental method details for a structure
Get ligand monomers on EBI PDBe
Returns chemical component IDs, names, molecular formulas, molecular weights, and their chain/residue positions. Essential for drug discovery and understanding protein-small molecule interactions. Get small molecule ligands bound in the structure
Get modified residues on EBI PDBe
Shows the parent compound ID and modification name. Get non-standard amino acids and nucleotides
Get molecules on EBI PDBe
Returns entity IDs, molecule types, names, chain assignments, sequence lengths, molecular weights, source organisms, and gene names. Get molecular entities (chains, polymers) in a structure
Get mutated residues on EBI PDBe
Shows the original residue, mutated residue, chain, and position. Essential for understanding how the crystallized construct differs from the native protein. Get engineered mutations vs. wild-type sequence
Get publications on EBI PDBe
Useful for finding the primary citation and methodology papers for a structure. Get associated journal publications and PubMed IDs
Get quality scores on EBI PDBe
The first thing a structural biologist checks when evaluating a structure for reliability. Get global quality metrics for a structure
Get related entries on EBI PDBe
Useful for discovering alternative conformations, mutants, or complexes of the same protein that have been structurally characterized. Get related PDB entries citing the same publications
Get residue listing on EBI PDBe
Shows residue names, numbers (both PDB and author numbering), organized by entity and chain. Returns a sample of the first 20 residues per chain for efficiency. Get full residue-level inventory per chain
Get secondary structure on EBI PDBe
Shows the count of helices and strands per chain, organized by molecular entity. Essential for understanding protein fold topology. Get helix, sheet, and coil assignments per residue
Get summary on EBI PDBe
Use a 4-character PDB ID such as 1cbs, 4hhb, 6lu7. Get PDB entry summary with title, authors, and resolution
Get uniprot mapping on EBI PDBe
Returns UniProt accessions, chain assignments, and start/end position mappings. Essential for cross-referencing between protein sequence databases and 3D structural data. Get UniProt to PDB residue mappings
Search structures on EBI PDBe
Use natural language queries like "insulin receptor kinase", "SARS-CoV-2 spike protein", "cryo-EM resolution<3", or specific organism names. Returns PDB IDs, titles, methods, resolutions, and organisms. Search PDB structures with full-text queries
Connect EBI PDBe to Claude Code via MCP
Follow these steps to wire EBI PDBe into Claude Code. The entire setup takes under two minutes — your credentials stay safe behind Vinkius.
Install Claude Code
npm install -g @anthropic-ai/claude-code if not already installedAdd the MCP Server
Verify the connection
claude mcp to list connected servers, or type /mcp inside a sessionStart using EBI PDBe
Why Use Claude Code with the EBI PDBe MCP Server
Claude Code provides unique advantages when paired with EBI PDBe 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 EBI PDBe 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
EBI PDBe + Claude Code Use Cases
Practical scenarios where Claude Code combined with the EBI PDBe MCP Server delivers measurable value.
CI/CD integration: embed EBI PDBe tool calls in your deployment pipeline to validate configurations or fetch secrets before shipping
Headless batch processing: schedule Claude Code to query EBI PDBe nightly and generate reports without human intervention
Shell scripting: pipe EBI PDBe outputs into other CLI tools for data transformation, filtering, and aggregation
Infrastructure monitoring: run Claude Code in a cron job to query EBI PDBe status endpoints and alert on anomalies
Example Prompts for EBI PDBe in Claude Code
Ready-to-use prompts you can give your Claude Code agent to start working with EBI PDBe immediately.
"Show me the structure summary and quality of the SARS-CoV-2 main protease (6lu7)."
"What ligands are bound in the hemoglobin structure 4hhb?"
"Search for cryo-EM structures of ribosome complexes."
Troubleshooting EBI PDBe MCP Server with Claude Code
Common issues when connecting EBI PDBe to Claude Code through Vinkius, and how to resolve them.
Command not found: claude
npm install -g @anthropic-ai/claude-codeConnection timeout
EBI PDBe + Claude Code FAQ
Common questions about integrating EBI PDBe 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.Explore More MCP Servers
View all →
Pitchly
11 toolsTurn your firm experience data into competitive deal sheets, credentials, and pitch materials with automated content generation.
Amazon EventBridge Bus
1 toolsEvent-driven architecture for AI agents — scoped event dispatching strictly limited to one EventBus for zero-trust security.
Treblle
1 toolsMonitor, document, and analyze your API traffic in real-time. Ingest request and response data directly into Treblle for instant observability.
Blackboard Learn
20 toolsManage courses, announcements, attendance, and grades directly from your AI agent via Blackboard Learn.