PDB-MCP-Server vs filesystem
Side-by-side comparison to help you pick between these two MCP servers.
PDB-MCP-Server by Augmented-Nature | filesystem by modelcontextprotocol | |
|---|---|---|
| Stars | ★ 24 | ★ 85,748 |
| 30d uses | — | — |
| Score | 42 | 77 |
| Official | — | ✓ |
| Categories | Knowledge GraphAI / LLM ToolsDeveloper Tools | File SystemDeveloper ToolsProductivity |
| Language | JavaScript | TypeScript |
| Last commit | 5 mo ago | this month |
PDB-MCP-Server · Summary
An MCP server providing access to Protein Data Bank structures with search, retrieval and download capabilities.
filesystem · Summary
A feature-rich MCP server for filesystem operations with dynamic directory access control.
PDB-MCP-Server · Use cases
- Structural biologists researching protein structures for drug discovery
- Scientists analyzing macromolecular assemblies and their interactions
- Educational institutions providing access to structural biology datasets
filesystem · Use cases
- Enable AI models to read and write project files during development
- Allow Claude or other MCP clients to browse and analyze codebases
- Provide secure sandboxed access to specific directories for content generation
PDB-MCP-Server · Install
npm install
npm run buildWith Claude Desktop, add to your claude_desktop_config.json:
{
"mcpServers": {
"pdb-server": {
"command": "node",
"args": ["/path/to/pdb-server/build/index.js"]
}
}
}filesystem · Install
Installation
Using NPX
{
"mcpServers": {
"filesystem": {
"command": "npx",
"args": [
"-y",
"@modelcontextprotocol/server-filesystem",
"/path/to/allowed/directory"
]
}
}
}Using Docker
{
"mcpServers": {
"filesystem": {
"command": "docker",
"args": [
"run",
"-i",
"--rm",
"--mount", "type=bind,src=/path/to/allowed/dir,dst=/projects/allowed/dir",
"mcp/filesystem",
"/projects"
]
}
}
}VS Code Extension
Click the installation buttons in the README to install directly in VS Code.