Uniprot vs MCP Server Neon
A side-by-side look at the Uniprot and MCP Server Neon MCP servers: transport, auth, tools, quality signals, and the config to install either one in Claude, Cursor, Windsurf or VS Code.
Verdict: choose Uniprot for databases work as a local process; choose MCP Server Neon for databases as a local process. You can also run both side by side in one mcpServers block.
Which MCP server should you choose?
Choose Uniprot when
- You need dedicated capabilities in the Databases domain.
- You prefer a local stdio subprocess transport.
- You want tools like
search, get, proteomes_search.
Choose MCP Server Neon when
- You need dedicated capabilities in the Databases domain.
- You prefer a local stdio subprocess transport.
- Its auth model fits you: OAuth 2.0.
- You have the keys it needs:
NEON_API_KEY. - You want tools like
projects, branches, endpoints.
Feature & specification comparison
Rows where the two servers differ are marked.
| Spec | ||
|---|---|---|
| Category | Databases | Databases |
| Quality signal | 57/100 · Good | 67/100 · Great |
| Install command | Confirmed | Confirmed |
| Transport | Local subprocess (stdio) | Local subprocess (stdio) |
| Auth | Not declared | OAuth 2.0 |
| Pricing | Not declared | Freemium |
| Required env vars | None listed | NEON_API_KEY |
| Verified owner | Community listing | Community listing |
| GitHub stars | 0 | 654 |
| Directory activity | 1 views 0 installs 0 upvotes | 5 views 0 installs 0 upvotes |
| Tools | 6 | 80 |
| Full listing | View Uniprot | View MCP Server Neon |
Tools & capabilities
Uniprot tools 6
search"Find protein [name]" / "look up [gene] in UniProt" / "BRCA1 / TP53 / insulin protein info" / "all proteins for [organism]" — UniProtKB search via Lucene-style queries (e.g. gene:BRCA1 AND organism_id:9606 for human BRCA1). UniProt is the authoritative protein-sequence-and-function database — use for protein characterization, function annotation, sequence retrieval, and cross-references to PDB/GO/PubMed.get"Fetch protein [P12345]" / "UniProt entry for [accession]" / "FASTA sequence for [protein]" — single UniProtKB entry by accession (e.g. P12345 or P38398 for BRCA1_HUMAN). Returns full protein record: sequence, function annotations, GO terms, cross-refs, post-translational modifications, variants. Pass format=fasta for sequence only.proteomes_search"Reference proteome for [organism]" / "complete protein set of [species]" — search UniProt reference proteomes (the curated representative protein set per organism). Use as a starting point for genome-scale protein analyses.taxonomy_search"NCBI taxonomy ID for [organism]" / "taxid for [species]" / "look up [Latin name] in NCBI taxonomy" — search NCBI Taxonomy via UniProt's mirror. Returns taxonomic IDs you can use as organism_id filters in `search` (9606 = human, 10090 = mouse, 7227 = D. melanogaster, etc).keyword"UniProt keyword KW-N info" / "what does keyword [X] mean" — fetch a UniProt controlled-vocabulary keyword by ID. Use to look up annotation tags like "Kinase" / "Membrane" / "Disease-associated".feature_summary"Domain map of [protein]" / "annotated features of [accession]" / "what regions / sites does [protein] have" — annotated features (domains, active sites, transmembrane regions, mutagenesis sites, glycosylation, disulfide bonds, etc.) for a UniProt accession. Use for structural/functional analysis without pulling the full protein record.
MCP Server Neon tools 80
projectsbranchesendpointssnapshotsschemaqueryingneon_authdata_apiobservabilitydocsfunctionsstorage- +68 more on 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.
Uniprot
{
"mcpServers": {
"uniprot": {
"command": "npx",
"args": [
"-y",
"@pipeworx/mcp-uniprot"
]
}
}
}
MCP Server Neon
{
"mcpServers": {
"neondatabase-mcp-server-neon": {
"command": "npx",
"args": [
"-y",
"neon@latest"
],
"env": {
"NEON_API_KEY": "YOUR_NEON_API_KEY_HERE"
}
}
}
}
Frequently asked questions
Uniprot is categorized under Databases and uses a local stdio subprocess. MCP Server Neon belongs to Databases and uses a local stdio subprocess. Pick Uniprot for databases work and MCP Server Neon for databases.
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.
Uniprot has no declared pricing — check the project's own site. MCP Server Neon is listed as freemium — a free tier with paid plans. Auth: oauth 2.0. 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 uniprot and neondatabase-mcp-server-neon as separate keys in the same mcpServers object, and your assistant will call tools from either one.
On AllMCPs, Uniprot has a quality signal of 57/100 (Good) with 1 views, 0 installs and 0 GitHub stars. MCP Server Neon has 67/100 (Great) with 5 views, 0 installs and 654 GitHub stars.