EBI PDBe MCP Server for ClineGive Cline instant access to 16 tools to Get Assemblies, Get Binding Sites, Get Cofactors, and more
GDPR Free for SubscribersCline is an autonomous AI coding agent inside VS Code that plans, executes, and iterates on tasks. Wire EBI PDBe through Vinkius and Cline gains direct access to every tool. from data retrieval to workflow automation. without leaving the terminal.
Ask AI about this MCP Server for Cline
The EBI PDBe MCP Server for Cline is a standout in the The Unthinkable category — giving your AI agent 16 tools to work with, ready to go from day one.
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"ebi-pdbe": {
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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.
Cline operates autonomously inside VS Code. it reads your codebase, plans a strategy, and executes multi-step tasks including EBI PDBe tool calls without waiting for prompts between steps. Connect 16 tools through Vinkius and Cline can fetch data, generate code, and commit changes in a single autonomous run.
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 Cline 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 Cline
When Cline 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 Cline via MCP
Follow these steps to wire EBI PDBe into Cline. The entire setup takes under two minutes — your credentials stay safe behind Vinkius.
Open Cline MCP Settings
Add remote server
Enable the server
Start using EBI PDBe
Why Use Cline with the EBI PDBe MCP Server
Cline provides unique advantages when paired with EBI PDBe through the Model Context Protocol.
Cline operates autonomously. it reads your codebase, plans a strategy, and executes multi-step tasks including MCP tool calls without step-by-step prompts
Runs inside VS Code, so you get MCP tool access alongside your existing extensions, terminal, and version control in a single window
Cline can create, edit, and delete files based on MCP tool responses, enabling end-to-end automation from data retrieval to code generation
Transparent execution: every tool call and file change is shown in Cline's activity log for full visibility and approval before committing
EBI PDBe + Cline Use Cases
Practical scenarios where Cline combined with the EBI PDBe MCP Server delivers measurable value.
Autonomous feature building: tell Cline to fetch data from EBI PDBe and scaffold a complete module with types, handlers, and tests
Codebase refactoring: use EBI PDBe tools to validate live data while Cline restructures your code to match updated schemas
Automated testing: Cline fetches real responses from EBI PDBe and generates snapshot tests or mocks based on actual payloads
Incident response: query EBI PDBe for real-time status and let Cline generate hotfix patches based on the findings
Example Prompts for EBI PDBe in Cline
Ready-to-use prompts you can give your Cline 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 Cline
Common issues when connecting EBI PDBe to Cline through Vinkius, and how to resolve them.
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EBI PDBe + Cline FAQ
Common questions about integrating EBI PDBe MCP Server with Cline.
How does Cline connect to MCP servers?
Can Cline run MCP tools without approval?
Does Cline support multiple MCP servers at once?
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