What is the key difference between Pubmed MCP Server and RCSB PDB?

Pubmed MCP Server belongs to the Biology & Bioinformatics category with local stdio execution, while RCSB PDB belongs to the Biology & Bioinformatics category with local stdio execution.

How do I install Pubmed MCP Server or RCSB PDB in Claude Desktop or Cursor?

Copy the mcpServers JSON configuration snippet provided on this page into your claude_desktop_config.json or ~/.cursor/mcp.json file and restart your AI client.

Are Pubmed MCP Server and RCSB PDB free or paid?

Pubmed MCP Server operates under a Free / Open Source model (No auth required). RCSB PDB operates under a Free / Open Source model (No auth required).

Which MCP server has more tools and community activity?

Pubmed MCP Server lists 0 tools with 0 views and 147 GitHub stars. RCSB PDB lists 35 tools with 0 views and 3 GitHub stars.

Can I use both Pubmed MCP Server and RCSB PDB together in the same MCP host?

Yes! MCP hosts like Claude Desktop, Cursor, Windsurf, Cline, and VS Code support configuring multiple servers under the mcpServers object simultaneously.

Side-by-Side Model Context Protocol Comparison

Pubmed MCP Server vs RCSB PDB

In-depth architectural comparison of the Pubmed MCP Server and RCSB PDB MCP servers. Compare execution transports, security boundaries, tool capabilities, quality scores, and ready-to-paste client installation snippets for Claude, Cursor, Windsurf, and VS Code.

At a Glance & Executive Verdict

Pubmed MCP Server

Biology & Bioinformatics · Local stdio

Quality: 41/100 (Fair) | Auth: No auth required

RCSB PDB

Biology & Bioinformatics · Local stdio

Quality: 53/100 (Good) | Auth: No auth required

Verdict Summary: Choose Pubmed MCP Server if you need specialized Biology & Bioinformatics tools running via a local process. Choose RCSB PDB if your workspace requires Biology & Bioinformatics integration with local subprocess execution. Both servers can be configured concurrently in your client's mcpServers manifest.

Which MCP Server Should You Choose?

Choose Pubmed MCP Server when:

You need dedicated capabilities in the Biology & Bioinformatics domain.
You prefer local stdio subprocess transport architecture.
Your security boundary fits: No auth required (Free / Open Source).

Explore Pubmed MCP Server Details

Choose RCSB PDB when:

You need dedicated capabilities in the Biology & Bioinformatics domain.
You prefer local stdio subprocess transport architecture.
Your security boundary fits: No auth required (Free / Open Source).
Primary tools included: rcsb_list_pdb_search_attributes, rcsb_find_go_terms, rcsb_find_interpro_domains.

Explore RCSB PDB Details

Feature & Specification Comparison

Specification	Pubmed MCP Server Biology & Bioinformatics	R RCSB PDB Biology & Bioinformatics
Summary	Comprehensive PubMed MCP Server to search, retrieve, and analyze biomedical literature from NCBI.	MCP server to search, inspect, and cross-reference RCSB Protein Data Bank structures
Category & Scope	Biology & Bioinformatics	Biology & Bioinformatics

Tools & Capabilities Breakdown

Pubmed MCP Server Tools (0)

No explicit tool names declared in metadata yet. Check project README on main listing page.

RCSB PDB Tools (35)

rcsb_list_pdb_search_attributes

Discover searchable attribute paths, types, and operators. `schema="structure"` (default, ~677) or `schema="chemical"` (~57: `chem_comp.*`, `drugbank_info.*`, ...).

rcsb_find_go_terms

Resolve a free-text molecular function / biological process / cellular component to Gene Ontology ids (via EBI QuickGO), annotated with PDB entry counts — then search by `rcsb_polymer_entity_annotation.annotation_lineage.id`.

rcsb_find_interpro_domains

Resolve a free-text protein domain / family / fold to InterPro ids (via EBI InterPro API), annotated with PDB entry counts — then search by `rcsb_polymer_entity_annotation.annotation_id`.

rcsb_find_enzyme_classes

Resolve a free-text enzyme / reaction to Enzyme Commission (EC) numbers (via EBI Search/IntEnz), annotated with PDB entry counts — then search by `rcsb_polymer_entity.rcsb_ec_lineage.id` (hierarchical).

Ready-to-Paste Client Configurations

Paste either (or both) of these JSON server blocks into your client config file (e.g. claude_desktop_config.json or ~/.cursor/mcp.json).

Pubmed MCP Server Configuration

mcpServers (Claude Desktop / Cursor)

{
  "mcpServers": {
    "pubmed-mcp-server-2": {
      "command": "bunx",
      "args": [
        "@cyanheads/pubmed-mcp-server@latest"
      ]
    }
  }
}

RCSB PDB Configuration

mcpServers (Claude Desktop / Cursor)

{
  "mcpServers": {
    "rcsb-pdb-2": {
      "command": "uvx",
      "args": [
        "rcsb-mcp"
      ]
    }
  }
}

Frequently Asked Questions

Pubmed MCP Server is categorized under Biology & Bioinformatics and uses a local stdio subprocess. In contrast, RCSB PDB belongs to Biology & Bioinformatics using local stdio subprocess. Select Pubmed MCP Server when you need capabilities focused on biology & bioinformatics and RCSB PDB when you require tools for biology & bioinformatics.

More alternatives to Pubmed MCP Server More alternatives to RCSB PDB Biology & Bioinformatics category hub