Alphafold vs Puumed
A side-by-side look at the Alphafold and Puumed MCP servers: transport, auth, tools, quality signals, and the config to install either one in Claude, Cursor, Windsurf or VS Code.
Verdict: choose Alphafold for biology & bioinformatics work as a local process; choose Puumed for biology & bioinformatics as a local process. You can also run both side by side in one mcpServers block.
Which MCP server should you choose?
Choose Alphafold when
- You need dedicated capabilities in the Biology & Bioinformatics domain.
- You prefer a local stdio subprocess transport.
- You want tools like
prediction.
Choose Puumed when
- You need dedicated capabilities in the Biology & Bioinformatics domain.
- You prefer a local stdio subprocess transport.
Feature & specification comparison
Rows where the two servers differ are marked.
| Spec | ||
|---|---|---|
| Category | Biology & Bioinformatics | Biology & Bioinformatics |
| Quality signal | 52/100 · Good | 40/100 · Fair |
| Install command | Confirmed | Confirmed |
| Transport | Local subprocess (stdio) | Local subprocess (stdio) |
| Auth | Not declared | Not declared |
| Pricing | Not declared | Not declared |
| Required env vars | None listed | None listed |
| Verified owner | Community listing |
Tools & capabilities
Alphafold tools 1
prediction
Puumed tools
No tool names declared yet. Check the project README from the listing page.
Ready-to-paste client configs
Paste either block (or both) into your client config, e.g. claude_desktop_config.json or ~/.cursor/mcp.json. We only show a config when the install command is confirmed.
Alphafold
{
"mcpServers": {
"alphafold": {
"command": "npx",
"args": [
"-y",
"@pipeworx/mcp-alphafold"
]
}
}
}
Puumed
{
"mcpServers": {
"puumed": {
"command": "npx",
"args": [
"-y",
"@pipeworx/mcp-pubmed"
]
}
}
}
Frequently asked questions
Alphafold is categorized under Biology & Bioinformatics and uses a local stdio subprocess. Puumed belongs to Biology & Bioinformatics and uses a local stdio subprocess. Pick Alphafold for biology & bioinformatics work and Puumed for biology & bioinformatics.
Copy the mcpServers block from the config section on this page into your client's config (for example claude_desktop_config.json or ~/.cursor/mcp.json), then fully restart the client.
Alphafold has no declared pricing — check the project's own site. Puumed has no declared pricing — check the project's own site. If a server needs environment variables such as API keys, define them under the env key in your client's MCP config.
Yes. MCP clients support multiple servers: add alphafold and puumed as separate keys in the same mcpServers object, and your assistant will call tools from either one.
On AllMCPs, Alphafold has a quality signal of 52/100 (Good) with 0 views, 0 installs and 1 GitHub stars. Puumed has 40/100 (Fair) with 1 views, 0 installs and 1 GitHub stars.