search_pubchem_by_nameLABSCO SUMMARY
Chemical facts from the source, not from the model.
Molecular weights and identifiers are exactly the kind of number a language model will produce confidently and get slightly wrong. Routing the question to PubChem means the property in the answer is the one on record, and a SMILES string works as the query when the name is ambiguous.
What it is
A lookup against PubChem, the public chemical database. A compound can be named in words or given as a SMILES string, and what comes back is its identifiers, structure and recorded properties.
What you get
- Compound search by common or systematic name
- Compound search by SMILES, for a structure you already have in hand
- Molecular structures and the identifiers that go with them
- The chemical and physical properties PubChem records for a compound
- A cap on how many results come back, so a broad name does not flood the answer
Requirements
Python on your PATH. No account and no key — PubChem is open.
Setup effort
One command — uv tool install pubchem-mcp-server
USE CASES
01
Getting the properties of a compound you can name
Ask by name and read back PubChem's recorded identifiers and properties, instead of trusting a figure the assistant recalled.
02
Identifying a structure you already have
Hand over the SMILES string and let PubChem tell you what it is — the reliable path when a name is ambiguous or the compound has several.
03
Comparing two candidates side by side
Look each one up in turn and put the recorded properties next to each other, so the comparison rests on database values rather than recollection.
04
Keeping a broad search readable
A common name can match a long list. Cap the number of results so the answer stays short enough to read and you can narrow from there.
4 tools
Listed in project docs. Your client may show a different list.
search_pubchem_by_smilesget_pubchem_compound_by_cidsearch_pubchem_advancedBEFORE YOU INSTALL
What to know first
Tools you get
4 tools named in the project's documentation.
Requires
Python 3.10+
Where it runs
Both documented clients run the server on your machine.
INSTALLATION
Connect your client
Server setup
Setup
TERMINAL
git clone https://github.com/JackKuo666/PubChem-MCP-Server.git
cd PubChem-MCP-Server
uv venv
source .venv/bin/activate
uv pip install -r requirements.txtuv
TERMINAL
uv tool install pubchem-mcp-serverMCP Clients
Claude Desktop
CLAUDE DESKTOP · JSON
{
"mcpServers": {
"pubchem": {
"command": "<YOUR_PATH_TO_PUB_CHEM_MCP_SERVER>/.venv/bin/python",
"args": [
"<YOUR_PATH_TO_PUB_CHEM_MCP_SERVER>/pubchem_server.py"
]
}
}
}<YOUR_PATH_TO_PUB_CHEM_MCP_SERVER> is the full path of the folder the clone created. .venv is the environment uv venv made there.
Cline
CLINE · JSON
{
"mcpServers": {
"pubchem": {
"command": "bash",
"args": [
"-c",
"source /home/<YOUR_USERNAME>/PATH/mcp-hub/PubChem-MCP-Server/.venv/bin/activate && python /home/<YOUR_USERNAME>/PATH/mcp-hub/PubChem-MCP-Server/pubchem_server.py"
],
"env": {},
"disabled": false,
"autoApprove": []
}
}
}The folder path in args appears twice, before /.venv/bin/activate and before /pubchem_server.py: both are the full path of the PubChem-MCP-Server folder you cloned, where the steps above create .venv.
