Bring Pdb
to OpenAI Agents SDK
Learn how to connect EBI PDBe to OpenAI Agents SDK and start using 16 AI agent tools in minutes. Fully managed, enterprise secure, and ready to use without writing a single line of code.
GDPR Free for SubscribersCompatible with every major AI agent and IDE
Gemini
What is the 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.
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
How it works
- Subscribe to this server
- No API key required — the PDBe API is fully public
- Start querying 3D structures from Claude, Cursor, or any MCP-compatible client
Your AI agent becomes a structural biology research assistant with direct access to every experimentally determined protein structure. All data is sourced from the official PDBe REST API maintained by EMBL-EBI.
Who is this for?
- Structural Biologists — retrieve structure metadata, quality assessments, and experimental parameters without downloading coordinate files
- Drug Discovery Scientists — identify binding sites, ligand interactions, and cofactors for rational drug design
- Bioinformaticians — cross-reference sequence data with 3D structural annotations via UniProt mappings
- Educators & Students — explore real macromolecular structures for teaching protein chemistry and structural biology
Built-in capabilities (16)
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)
Critical for drug discovery, molecular docking, and understanding protein-ligand interactions. Get ligand binding site residues and interactions
Cofactors like heme, NAD+, FAD, and metal ions are essential for enzyme catalysis and protein function. Get cofactor and prosthetic group annotations
Get experimental method details for a structure
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
Shows the parent compound ID and modification name. Get non-standard amino acids and nucleotides
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
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
Useful for finding the primary citation and methodology papers for a structure. Get associated journal publications and PubMed IDs
The first thing a structural biologist checks when evaluating a structure for reliability. Get global quality metrics for a structure
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
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
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
Use a 4-character PDB ID such as 1cbs, 4hhb, 6lu7. Get PDB entry summary with title, authors, and resolution
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
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
Why OpenAI Agents SDK?
The OpenAI Agents SDK auto-discovers all 16 tools from EBI PDBe through native MCP integration. Build agents with built-in guardrails, tracing, and handoff patterns. chain multiple agents where one queries EBI PDBe, another analyzes results, and a third generates reports, all orchestrated through Vinkius.
- —
Native MCP integration via
MCPServerSse, pass the URL and the SDK auto-discovers all tools with full type safety - —
Built-in guardrails, tracing, and handoff patterns let you build production-grade agents without reinventing safety infrastructure
- —
Lightweight and composable: chain multiple agents and MCP servers in a single pipeline with minimal boilerplate
- —
First-party OpenAI support ensures optimal compatibility with GPT models for tool calling and structured output
EBI PDBe in OpenAI Agents SDK
EBI PDBe and 4,000+ other MCP servers. One platform. One governance layer.
Teams that connect EBI PDBe to OpenAI Agents SDK through Vinkius don't need to source, host, or maintain individual MCP servers. Every tool call runs inside a hardened runtime with credential isolation, DLP, and a signed audit chain.
Raw MCP | Vinkius | |
|---|---|---|
| Server catalog | Find and host yourself | 4,000+ managed |
| Infrastructure | Self-hosted | Sandboxed V8 isolates |
| Credential handling | Plaintext in config | Vault + runtime injection |
| Data loss prevention | None | Configurable DLP policies |
| Kill switch | None | Global instant shutdown |
| Financial circuit breakers | None | Per-server limits + alerts |
| Audit trail | None | Ed25519 signed logs |
| SIEM log streaming | None | Splunk, Datadog, Webhook |
| Honeytokens | None | Canary alerts on leak |
| Custom domains | Not applicable | DNS challenge verified |
| GDPR compliance | Manual effort | Automated purge + export |
Why teams choose Vinkius for EBI PDBe in OpenAI Agents SDK
The EBI PDBe 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. All 16 tools execute in hardened sandboxes optimized for native MCP execution.
Your AI agents in OpenAI Agents SDK only access the data you authorize, with DLP that blocks sensitive information from ever reaching the model, kill switch for instant shutdown, and up to 60% token savings. Enterprise-grade infrastructure, zero maintenance.
* 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
How Vinkius secures
EBI PDBe for OpenAI Agents SDK
Every tool call from OpenAI Agents SDK to the EBI PDBe MCP Server is protected by DLP redaction, cryptographic audit chains, V8 sandbox isolation, kill switch, and financial circuit breakers.
Frequently asked questions
Do I need an API key?
No. The PDBe API is completely public and requires no authentication. Enter any placeholder value in the API key field to activate the server immediately.
What types of structures are available?
The PDBe contains over 200,000 experimentally determined 3D structures of proteins, nucleic acids, and complex assemblies. Structures are determined by X-ray crystallography, cryo-electron microscopy (cryo-EM), NMR spectroscopy, and other methods. This includes enzymes, receptors, antibodies, viral proteins, ribosomes, and drug-target complexes.
Can I find drug binding sites?
Yes. Use get_binding_sites to retrieve all annotated ligand binding pockets with their constituent residues. Combine with get_ligand_monomers to identify the small molecules bound in the structure, and get_cofactors for prosthetic groups. This workflow is essential for structure-based drug design and virtual screening target preparation.
How does the OpenAI Agents SDK connect to MCP?
Use MCPServerSse(url=...) to create a server connection. The SDK auto-discovers all tools and makes them available to your agent with full type information.
Can I use multiple MCP servers in one agent?
Yes. Pass a list of MCPServerSse instances to the agent constructor. The agent can use tools from all connected servers within a single run.
Does the SDK support streaming responses?
Yes. The SDK supports SSE and Streamable HTTP transports, both of which work natively with Vinkius.
MCPServerStreamableHttp not found
Ensure you have the latest version: pip install --upgrade openai-agents
Agent not calling tools
Make sure your prompt explicitly references the task the tools can help with.
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