Pdbe
PDBe (Protein Data Bank in Europe, EBI) MCP.
MCP server · by pipeworx-io
About
Pdbe is an MCP server published by pipeworx-io. Marketplaces we read that list it: 1 (Official MCP Registry). We first saw it on 2026-10-11 and have recorded no change since. As of our marketplace pass on 2026-10-13.
What it asks for
- Runs remotely
None of the marketplaces we read publishes its tools or the settings it asks for.
What it declares, asks for and runs, in full
Only install plugins from developers you trust. We list what marketplaces publish and do not test plugins.
Works with
- Claude Code
- Codex
- Cursor
- VS Code
- Copilot CLI
A one-click link opens the client, which asks you to confirm before it adds the server.
From the marketplaces that list it and the MCP transport it declares, as each client documents them. We do not test plugins.
Connect
Commands and configs built only from what its marketplaces declare. We do not run them for you and do not test plugins.
As a remote MCP server
Built from what Official MCP Registry declares.
claude mcp add --transport http pdbe https://gateway.pipeworx.io/pdbe/mcp
[mcp_servers.pdbe]
url = "https://gateway.pipeworx.io/pdbe/mcp"
{
"mcpServers": {
"pdbe": {
"url": "https://gateway.pipeworx.io/pdbe/mcp"
}
}
}
Where it is published
| Marketplace | Status | Version | Figures | Verified | First seen |
|---|---|---|---|---|---|
| Official MCP Registry (Open the registry record) | Listed | 0.1.2 | Forks (GitHub): 0 Stars (GitHub): 0 |
Not marked |
Each figure is the marketplace's own and is never added up across marketplaces. A marketplace that publishes no figure shows none: no number is not zero.
What changed
Nothing has moved on this plugin since we started watching it.
Similar plugins
Products whose own names, descriptions, tools and skills are closest in meaning to this one, on every marketplace we read. Closeness is ranked within this list only.
-
EMDB (EBI Electron Microscopy Data Bank) MCP — keyless.
-
RCSB PDB MCP — experimentally determined macromolecular structures.
-
EBI PRIDE Archive MCP — proteomics (mass-spectrometry) data repository.
-
PeeringDB MCP — the peering ecosystem database.
-
Paleobiology Database (PBDB) MCP — the global fossil record. Keyless.
-
UniProt MCP — protein sequence + function database.
-
protein-mcp-server io.github.cyanheads/protein-mcp-server
MCP Server for 3D protein structural data retrieval & analysis from RCSB PDB, PDBe, and UniProt.
-
ChEMBL MCP — drug discovery database (EBI).
-
AlphaFold DB MCP — predicted protein structures.
-
STRING-DB MCP — protein-protein interaction networks.
Similar plugins by marketplace
The same question asked of one marketplace at a time: is there an analog of this plugin there?
Has a listing on Claude Code: claude-plugins-community (5)
-
mdk-mcp-server io.github.SAP/mdk-mcp-server
Model Context Protocol (MCP) server for AI-assisted development of MDK applications.
-
Interactively explore MCP server tools and their input schemas. mcpx lets you drill down from server → tool → schema to understand what each tool expects. Browse all configured…
-
Multi-model deliberation over MCP: full responses plus typed cross-model reactions from other labs.
-
Zero-config MCP server for searchable documentation. SQLite or PostgreSQL.
-
mcp-server io.github.cap-js/mcp-server
Model Context Protocol (MCP) server for AI-assisted development of CAP applications.
Has a listing on Claude Code: claude-plugins-official (5)
-
mdk-mcp-server io.github.SAP/mdk-mcp-server
Model Context Protocol (MCP) server for AI-assisted development of MDK applications.
-
mcp-server io.github.cap-js/mcp-server
Model Context Protocol (MCP) server for AI-assisted development of CAP applications.
-
Skills for designing and building MCP servers that work seamlessly with Claude. Guides you through deployment models (remote HTTP, MCPB, local), tool design patterns, auth, and…
-
MCP server for terminal commands, file operations, and process management
-
An authenticated hosted MCP server that accesses your PlanetScale organizations, databases, branches, schema, and Insights data. Query against your data, surface slow queries, and…
Has a listing on Claude: knowledge-work-plugins (5)
-
MCP server for terminal commands, file operations, and process management
-
An authenticated hosted MCP server that accesses your PlanetScale organizations, databases, branches, schema, and Insights data. Query against your data, surface slow queries, and…
-
Figma design platform integration. Access design files, extract component information, read design tokens, and translate designs into code. Bridge the gap between design and…
-
Prisma MCP integration for Postgres database management, schema migrations, SQL queries, and connection string management. Provision Prisma Postgres databases, run migrations, and…
-
Search companies and contacts, enrich leads, find lookalikes, and get AI-ranked contact recommendations. Pre-built skills chain multiple ZoomInfo tools into complete B2B sales…
Has a listing on Codex: openai-curated (openai/plugins) (5)
-
Predict structures, screen molecules and proteins, and design binders.
-
General life-sciences research workflows with query routing, evidence synthesis, and optional parallel subagent analysis across genetics, omics, biology, chemistry, structure…
-
Manage Supabase projects directly through ChatGPT. Execute SQL queries on PostgreSQL databases, design and modify table schemas, deploy serverless edge functions, and configure…
-
Use MagicPath to find, inspect, install, create, and edit UI components from Codex.
-
Bring operational data and context into the flow of your ChatGPT conversations. You can ask questions, create and update records, and analyze your data—all through conversation…
Has a listing on Community GitHub marketplaces (5)
-
Build, audit and repair Power BI Desktop models and PBIP reports with DAX, TMDL and PBIR.
-
Database MCP server for schema discovery, comments, and SQL queries.
-
MCP bridge to the Tabellum database client: schema, reads, SQL drafts; writes approved in the app.
-
basicdeploy-mcp io.github.AkaciaNL/basicdeploy-mcp
The runtime your agent deploys to — DB, storage, and a public URL in one MCP call.
-
pbirb-mcp io.github.mafaq229/pbirb-mcp
MCP server for editing Power BI Report Builder paginated reports (RDL)
Has a listing on Copilot CLI: github/awesome-copilot (5)
-
Complete toolkit for building Model Context Protocol (MCP) servers in TypeScript/Node.js using the official SDK. Includes instructions for best practices, a prompt for generating…
-
Complete toolkit for building Model Context Protocol (MCP) servers in Go using the official github.com/modelcontextprotocol/go-sdk. Includes instructions for best practices, a…
-
Build Model Context Protocol (MCP) servers in Python with the official MCP Python SDK v2 (MCPServer). Includes a skill that generates a server project and an expert agent for…
-
Comprehensive resources for building Model Context Protocol servers using the official PHP SDK with attribute-based discovery, including best practices, project generation, and…
-
Complete toolkit for building Model Context Protocol (MCP) servers in Kotlin using the official io.modelcontextprotocol:kotlin-sdk library. Includes instructions for best…
Has a listing on Copilot CLI: github/copilot-plugins (5)
-
mcp-apps
Generate MCP App widgets for MCP tools. Produces self-contained HTML widgets using the MCP Apps protocol.
-
power-automate
Build, edit, run, and debug Power Automate cloud flows via the FlowAgent MCP server — connection lifecycle, surgical edits, copy across environments, run management, and validated…
-
Build Power Apps Canvas Apps using the Canvas Authoring MCP server.
-
model-apps
Build and deploy Power Apps generative pages for model-driven apps with specialist agents for planning, entity creation, and parallel code generation. Requires PAC CLI >= 2.7.0…
-
code-apps-preview
Build and deploy Power Apps code apps using React, Vite, and Power Platform connectors.
Has a listing on Cursor: cursor/plugins (5)
-
Let Grok Bot reach MCP servers on your private Tailscale network. Sign in to Tailscale to connect your tailnet; Grok Bot joins it as one tagged device and only reaches the hosts…
-
Work with PostHog from chat: query product analytics and run SQL, manage feature flags and experiments, triage error tracking issues, and review session replays, surveys, and…
-
Search docs, read pages, and update tables.
-
Build apps, scripts, and automations with the TypeScript SDK.
-
if you want to go fast, go deep first. pstack helps you write less, but higher quality code. rigorous agent workflows you can parallelize with confidence.
Has a listing on Docker MCP Catalog (5)
-
Official ClickHouse MCP server for querying and exploring ClickHouse clusters and chDB.
-
Remote MCP server for the Hackle Admin API: experiments, feature flags, remote config, messaging.
-
Dynatrace-mcp io.github.dynatrace-oss/Dynatrace-mcp
[DEPRECATED] Dynatrace MCP Server. Migrate to dynatrace-for-ai or Dynatrace Remote MCP Server.
-
Access to Rube's catalog of remote MCP servers.
-
mcp-server-couchbase io.github.Couchbase-Ecosystem/mcp-server-couchbase
Couchbase Model Context Protocol Server to interact with Couchbase clusters
Has a listing on Official MCP Registry (5)
-
EMDB (EBI Electron Microscopy Data Bank) MCP — keyless.
-
RCSB PDB MCP — experimentally determined macromolecular structures.
-
EBI PRIDE Archive MCP — proteomics (mass-spectrometry) data repository.
-
PeeringDB MCP — the peering ecosystem database.
-
Paleobiology Database (PBDB) MCP — the global fossil record. Keyless.
Found by meaning, not by shared code or a shared repository: similar plugins stay separate products, and this is not a review or a recommendation.
Is this your plugin?
Add it to your projects and prove you maintain it with a file in its repository, a file on your domain or a DNS record. You get alerts when a marketplace lists it, drops it, changes its verified mark or what it asks for, and its remote endpoint goes on monitoring as a web service.
Data comes from the Official MCP Registry (registry.modelcontextprotocol.io), CC0 1.0. Figures come from our own regular passes over the marketplaces, last read on . We publish no contact details for plugin publishers.