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Vinkius

RCSB PDB Connector for AI agents.

2 live capabilities

Query experimental 3D molecular structures for drug discovery and structural biology research.

Live agent request RCSB PDB / Connector

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AI Agent

Why people use RCSB PDB

RCSB PDB for Faster Drug Discovery Research

With this Connector, you just tell your agent what you're looking for. It pulls the resolution, the experimental method, and the bound molecules into a single response. You get the data you need without ever leaving your workspace.

  • Claude
  • ChatGPT
  • Gemini
  • Cursor
  • Visual Studio Code
  • Windsurf

What Vinkius changes

You get instant access to experimental 3D structural data without leaving your chat interface.

Use it from Claude, ChatGPT, Cursor or another AI client you already have.

One account · 5,900+ Connectors

  1. Real-world use case 01

    Finding a specific target

    A researcher needs the structure of the SARS-CoV-2 protease.

  2. Real-world use case 02

    Validating experimental data

    A biologist wants to know the resolution of a hemoglobin structure.

  3. Real-world use case 03

    Filtering by technique

    A team needs only Cryo-EM structures of ribosomes.

Complete set · 2capabilities

The complete RCSB PDB capability set.

These are the exact actions your AI can choose when you ask it to work with RCSB PDB.

Capability set01 / 01

01—02

2 capabilities in this set.

Part of 2 available through RCSB PDB.

  1. 01 Capability

    Get pdb structure

    Fetch full structural details, including experimental methods and bound molecules, using a 4-character PDB ID. This is useful for getting precise metadata for a known target.

  2. 02 Capability

    Search pdb

    Search the Protein Data Bank for structures based on names, diseases, or experimental techniques like Cryo-EM. Use this to discover new structures or filter by resolution.

Set up in minutes

One URL. Then ask RCSB PDB to work.

Claude and ChatGPT only need the Connector URL. Copy it once, add it in settings, and use RCSB PDB from the conversation.

Choose your client

Live preview
Advanced clients IDE · CLI

Claude · Web + desktop

Official guide ↗

Connector URL · ready to paste

Streamable HTTP
https://edge.vinkius.com/vk_preview_px4KJXLkPAfRiw8dj06D8ILeCL0RIsHNqISA0zQD/mcp
  1. Step 01

    Open Connectors

    In Claude Web or Claude Desktop, open Settings and choose Connectors.

  2. Step 02

    Add the URL

    Choose Add custom connector, name it RCSB PDB, and paste the URL above.

  3. Step 03

    Turn it on in chat

    Select +, open Connectors, and enable RCSB PDB for the conversation.

Where the request belongs

Work RCSB PDB can move forward.

Built around the request

This is for researchers who spend hours digging through structural databases to find the right protein models or ligand data. It solves the friction of manual data entry and tab-switching for those who need high-fidelity structural info for publication or lab work.

01

Structural Biologist

Pulls metadata on experimental methods and resolutions to verify data quality for a publication.

02

Drug Discovery Researcher

Finds protein-ligand co-crystal structures to guide virtual screening and lead optimization.

03

Biochemistry Student

Explores real 3D structures of DNA and RNA to visualize molecular architecture for a thesis.

Build the capability set

Add more capabilities.

Each Connector adds new actions and data without changing how you work.

Browse Connectors
EBI PDBe logo
01 16 capabilities

EBI PDBe

Explore 3D protein structures, ligand interactions, and molecular assemblies from the Protein Data Bank in Europe.

View Connector
UniProt logo
02 3 capabilities

UniProt

Search 250M+ protein sequences with functional annotations, gene names, subcellular locations, and amino acid data from the world's most comprehensive protein knowledge base.

View Connector
EBI Proteins API logo
03 16 capabilities

EBI Proteins API

Query the UniProt knowledge base for protein sequences, annotations, and functional data across millions of characterized entries.

View Connector
EBI InterPro logo
04 16 capabilities

EBI InterPro

Classify protein sequences into families, predict functional domains, and explore evolutionary relationships across species.

View Connector
PubChem logo
05 3 capabilities

PubChem

Search 116M+ chemical compounds with molecular properties, SMILES notation, formulas, and drug-like properties from the world's largest free chemistry database.

View Connector
GenBank/NCBI API logo
06 4 capabilities

GenBank/NCBI API

Access genomic data. audit sequences, proteins, and UIDs via IA.

View Connector

Bring your own AI

Change the model, client or framework. Keep RCSB PDB connected.

  • Claude
  • ChatGPT
  • Gemini
  • Cursor
  • VS Code
  • Windsurf
  • ZCode
  • Cline
  • Zed
  • Continue
  • Kiro
  • Roo Code
  • Zencoder
  • Goose
  • Void
  • Augment Code
  • Amp
  • Qodo
  • Tabnine
  • Pieces
  • Sourcegraph Cody
  • JetBrains
  • Warp
  • Amazon Q
  • Antigravity
  • BoltAI
  • Raycast
  • Jan
  • LM Studio
  • AnythingLLM
  • Open WebUI
  • Msty
  • Cherry Studio
  • LibreChat
  • TypingMind
  • Chorus
  • 5ire
  • n8n
  • LangChain
  • LlamaIndex
  • CrewAI
  • Vercel AI SDK

Before you connect

Questions about RCSB PDB.

The practical details behind the request, access and result.

Can the RCSB PDB MCP find specific protein structures?

Yes, it can search over 220,000 entries by name, function, or disease association to find the exact 3D structure you need.

How do I get experimental details like resolution using the RCSB PDB MCP?

Your agent can pull the resolution, experimental method, and author details for any specific PDB ID instantly.

Does the RCSB PDB MCP support Cryo-EM and X-ray data?

Yes, it allows you to filter structures by their experimental method, including Cryo-EM, X-ray diffraction, and NMR.

Can I use the RCSB PDB MCP for drug discovery?

It's a great capability for drug discovery because it helps you identify bound ligands and co-crystal structures for virtual screening.

What kind of molecules can I find with the RCSB PDB MCP?

You can find 3D structural data for proteins, DNA, and RNA, along with information on bound ligands and cofactors.

Do I need an API key for the RCSB PDB MCP?

No, you don't need an API key to start searching for molecular structures through this Connector.

What experimental methods are represented in the PDB?

The PDB contains structures determined by four main methods: X-ray Crystallography (85% of entries, atomic resolution), Cryo-EM (rapidly growing, now 15%+ of new deposits), NMR Spectroscopy (solution-state structures), and Neutron Diffraction (hydrogen atom positions). Each entry lists its method and resolution.

Do I need authentication to access PDB data?

No. RCSB PDB is completely free and open. funded by NSF, NIH, DOE, and international partners. All 220K+ structures are openly accessible without any registration or API key. The data is licensed under CC0 (public domain).

What information does each PDB entry contain?

Each entry includes: PDB ID (4-character code), structure title, depositing authors, experimental method, resolution in Ångströms, source organism, release date, number of polymer chains, and bound non-polymer ligands (drugs, cofactors, ions). Higher resolution (lower number) means more precise atomic coordinates.

One connection away

Give your agent a direct line to RCSB PDB.

Connect RCSB PDB once. Keep it beside 5,900+ managed Connectors when the next task needs more.

Explore every Connector No credit card required · Free tier available