What is the key difference between Pymol MCP and Heor Agent MCP?

Pymol MCP belongs to the Biology, Medicine and Bioinformatics category with local stdio execution, while Heor Agent MCP belongs to the Biology, Medicine and Bioinformatics category with local stdio execution.

How do I install Pymol MCP or Heor Agent MCP 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 Pymol MCP and Heor Agent MCP free or paid?

Pymol MCP operates under a Free / Open Source model (No auth required). Heor Agent MCP operates under a Free / Open Source model (No auth required).

Which MCP server has more tools and community activity?

Pymol MCP lists 0 tools with 0 views and 0 GitHub stars. Heor Agent MCP lists 17 tools with 3 views and 9 GitHub stars.

Can I use both Pymol MCP and Heor Agent MCP 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

Pymol MCP vs Heor Agent MCP

In-depth architectural comparison of the Pymol MCP and Heor Agent MCP 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

Pymol MCP

Biology, Medicine and Bioinformatics · Local stdio

Quality: 43/100 (Fair) | Auth: No auth required

Heor Agent MCP

Biology, Medicine and Bioinformatics · Local stdio

Quality: 61/100 (Good) | Auth: No auth required

Verdict Summary: Choose Pymol MCP if you need specialized Biology, Medicine and Bioinformatics tools running via a local process. Choose Heor Agent MCP if your workspace requires Biology, Medicine and 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 Pymol MCP when:

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

Explore Pymol MCP Details

Choose Heor Agent MCP when:

You need dedicated capabilities in the Biology, Medicine and Bioinformatics domain.
You prefer local stdio subprocess transport architecture.
Your security boundary fits: No auth required (Free / Open Source).
Primary tools included: literature_search, screen_abstracts, risk_of_bias.

Explore Heor Agent MCP Details

Feature & Specification Comparison

Specification	Pymol MCP wjgoarxiv Biology, Medicine and Bioinformatics	Heor Agent MCP neptun2000 Biology, Medicine and Bioinformatics
Summary	Headless PyMOL for molecular visualization, GROMACS/LAMMPS MD trajectories, and clathrate-hydrate cage analysis: H-bond networks, F3/F4 order parameters, and TRACE cage perception + occupancy.	HEOR (Health Economics and Outcomes Research) MCP server with 7 tools for literature search across 41 medical data sources (PubMed, NICE, CADTH, ICER, etc.), cost-effectiveness modeling (Markov/PartSA/PSA), and HTA dossier preparation for pharmaceutical and biotech teams.
Category & Scope

Tools & Capabilities Breakdown

Pymol MCP Tools (0)

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

Heor Agent MCP Tools (17)

literature_search

Search 44 data sources with a full PRISMA-style audit trail

screen_abstracts

PICO-based relevance scoring and study design classification

risk_of_bias

Cochrane RoB 2 / ROBINS-I / AMSTAR-2 with GRADE RoB domain summary

evidence_network

Build treatment comparison network and assess NMA feasibility

evidence_indirect

Bucher and frequentist NMA with **automatic consistency check** vs direct h2h evidence (NICE DSU TSD 18)

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).

Pymol MCP Configuration

mcpServers (Claude Desktop / Cursor)

{
  "mcpServers": {
    "wjgoarxiv-pymol-mcp": {
      "command": "uvx",
      "args": [
        "wjgoarxiv-pymol-mcp"
      ]
    }
  }
}

Heor Agent MCP Configuration

mcpServers (Claude Desktop / Cursor)

{
  "mcpServers": {
    "neptun2000-heor-agent-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "heor-agent-mcp"
      ]
    }
  }
}

Frequently Asked Questions

Pymol MCP is categorized under Biology, Medicine and Bioinformatics and uses a local stdio subprocess. In contrast, Heor Agent MCP belongs to Biology, Medicine and Bioinformatics using local stdio subprocess. Select Pymol MCP when you need capabilities focused on biology, medicine and bioinformatics and Heor Agent MCP when you require tools for biology, medicine and bioinformatics.

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