EBI InterPro MCP Server for ClineGive Cline instant access to 16 tools to Get Cdd Entry, Get Clan, Get Entry, and more
GDPR Free for SubscribersCline is an autonomous AI coding agent inside VS Code that plans, executes, and iterates on tasks. Wire EBI InterPro 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 InterPro 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.
Vinkius delivers Streamable HTTP and SSE to any MCP client
Gemini{
"mcpServers": {
"ebi-interpro": {
"url": "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 InterPro 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 InterPro MCP Server
Connect to the InterPro API and access the world's most comprehensive resource for protein family, domain, and functional site classification.
Cline operates autonomously inside VS Code. it reads your codebase, plans a strategy, and executes multi-step tasks including EBI InterPro 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
- Domain Classification — Retrieve detailed InterPro entry information including family/domain descriptions, GO terms, and member database cross-references
- Multi-Database Access — Query entries from Pfam, CDD, SMART, Prosite, PANTHER, Gene3D, HAMAP, and more through a unified interface
- Protein Annotation — Find all InterPro domains, families, and sites annotated on any UniProt protein
- Structure Mapping — Discover PDB structures containing proteins that match specific InterPro entries
- Taxonomic Distribution — Explore which organisms contain proteins matching a domain or family — essential for evolutionary biology
- Proteome Coverage — Assess domain annotation coverage for complete proteomes
- Clan Analysis — Navigate Pfam clan hierarchies to understand super-family relationships
The EBI InterPro 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 InterPro tools available for Cline
When Cline connects to EBI InterPro through Vinkius, your AI agent gets direct access to every tool listed below — spanning interpro, pfam, protein-domains, 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 cdd entry on EBI InterPro
CDD provides curated models for protein domain families and includes additional alignment and structure data. Use accessions like cd00001. Get CDD (Conserved Domain Database) entry details
Get clan on EBI InterPro
Returns clan accession, name, description, and member counts. Use Pfam clan accessions like CL0001. Get Pfam clan (super-family grouping) details
Get entry on EBI InterPro
Returns name, type (family, domain, homologous superfamily, repeat, site), description, Gene Ontology terms, member database cross-references, and literature count. Use accessions like IPR000001, IPR036291. Get InterPro entry metadata for a family or domain
Get entry proteins on EBI InterPro
Returns protein accessions, names, lengths, and source organisms. Useful for finding all members of a protein family across the UniProt database. Get all proteins matching an InterPro entry
Get entry structures on EBI InterPro
Returns PDB IDs, names, experiment types, and resolutions. Useful for finding structural representatives of a protein family or domain. Get all PDB structures matching an InterPro entry
Get entry taxonomy on EBI InterPro
Returns taxonomy nodes with names, ranks, and protein counts. This answers the evolutionary biology question "which organisms have this domain/family?" and is essential for understanding protein evolution and conservation. Get taxonomic distribution of an InterPro entry
Get pfam entry on EBI InterPro
Pfam is the most widely used protein domain database. Use accessions like PF00069 (kinase domain), PF00076 (RRM domain). Get Pfam domain or family details
Get protein on EBI InterPro
Returns the protein name, length, source organism, evidence level, fragment status, and counters for how many InterPro entries, Pfam domains, structures, and taxa are associated with it. Get protein details with all domain and family assignments
Get protein entries on EBI InterPro
This is the key tool for understanding "what domains does my protein have?" — the fundamental question in protein characterization. Get all InterPro entries matching a specific protein
Get proteome on EBI InterPro
Returns proteome ID, organism name, strain, reference status, and counters for associated entries and proteins. Use UniProt proteome IDs like UP000005640 (human). Get proteome details with domain coverage statistics
Get structure on EBI InterPro
Use a 4-character PDB ID like 1cbs or 4hhb. Get a PDB structure with mapped InterPro annotations
Get taxonomy on EBI InterPro
Returns the organism name, rank, lineage, number of children taxa, and counters for associated InterPro entries and proteins. Use IDs like 9606 (human), 10090 (mouse), 562 (E. coli). Get taxonomic node with entry and protein counts
List entry databases on EBI InterPro
Shows the number of entries in each database. Useful for understanding the scope of available domain and family annotations. List all InterPro member databases and entry counts
Search entries on EBI InterPro
Optionally filter by entry type: family, domain, homologous_superfamily, repeat, or site. Returns accessions, names, types, and protein/structure counts. Use queries like "kinase", "zinc finger", "immunoglobulin". Search InterPro entries by keyword and type
Search proteins on EBI InterPro
Returns UniProt accessions, names, lengths, organisms, and annotation counts. Use queries like "insulin", "hemoglobin", "BRCA1". Search proteins in InterPro by name or keyword
Search taxonomy on EBI InterPro
Returns taxon IDs, names, ranks, and annotation counts. Use queries like "human", "drosophila", "arabidopsis", "saccharomyces". Search taxonomy by organism name
Connect EBI InterPro to Cline via MCP
Follow these steps to wire EBI InterPro 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 InterPro
Why Use Cline with the EBI InterPro MCP Server
Cline provides unique advantages when paired with EBI InterPro 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 InterPro + Cline Use Cases
Practical scenarios where Cline combined with the EBI InterPro MCP Server delivers measurable value.
Autonomous feature building: tell Cline to fetch data from EBI InterPro and scaffold a complete module with types, handlers, and tests
Codebase refactoring: use EBI InterPro tools to validate live data while Cline restructures your code to match updated schemas
Automated testing: Cline fetches real responses from EBI InterPro and generates snapshot tests or mocks based on actual payloads
Incident response: query EBI InterPro for real-time status and let Cline generate hotfix patches based on the findings
Example Prompts for EBI InterPro in Cline
Ready-to-use prompts you can give your Cline agent to start working with EBI InterPro immediately.
"What domains and families does the human TP53 protein belong to?"
"Show me all member databases in InterPro and how many entries each has."
"Which organisms have the kinase domain PF00069?"
Troubleshooting EBI InterPro MCP Server with Cline
Common issues when connecting EBI InterPro to Cline through Vinkius, and how to resolve them.
Server shows error in sidebar
EBI InterPro + Cline FAQ
Common questions about integrating EBI InterPro 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?
Explore More MCP Servers
View all →
Sapling (Kallidus)
10 toolsManage employee onboarding, data, and tasks via Sapling API.
TimezoneDB
5 toolsManage global time — audit timezones and offsets via AI.
Cognito Forms
12 toolsBuild smart online forms with conditional logic, calculations, and payment collection that adapt to every response.
REST Countries
6 toolsManage your global research — audit country records, currencies, and languages via AI.