← All skills
pubchem-compound-search
77 / 100 · Review before installing
Check before installing. Some of what it can do is expected: a coding skill usually runs build and test commands.
By BioTender-max/awesome-bio-agent-skills (GitHub) · coding · 219 stars · scanned at commit 8cbdd18
Query PubChem (110M+ compounds) directly via the PUG-REST/JSON API with plain `requests` — no SDK install required. Search by name/CID/SMILES/InChIKey/formula, retrieve properties (MW, XLogP, TPSA, H-bond counts), do similarity/substructure searches with async ListKey polling, fetch synonyms, descriptions, assay summaries, and download SDF/PNG. For local cheminformatics use rdkit; for bioactivity-centric workflows use chembl-database-bioactivity.
Works with any agent that supports SKILL.md skills.
What this skill can do
Downloads and installs other software
The author does not mention this.
Found in 1 place.
Runs commands on your computer
The author does not mention this. Expected for a coding skill.
Found in 1 place.
Sends data to these websites: pubchem.ncbi.nlm.nih.gov
This is disclosed by the author in the skill's SKILL.md or README.
Found in 32 places.
Show 17 more
- skills/sciagent/pubchem-compound-search/SKILL.md, line 89
cid = requests.get(f"{BASE}/compound/smiles/{smi}/cids/JSON").json()["IdentifierList"]["CID"][0] - skills/sciagent/pubchem-compound-search/SKILL.md, line 94
cid = requests.get(f"{BASE}/compound/inchikey/{ikey}/cids/JSON").json()["IdentifierList"]["CID"][0] - skills/sciagent/pubchem-compound-search/SKILL.md, line 111
p = requests.get(url).json()["PropertyTable"]["Properties"][0] - skills/sciagent/pubchem-compound-search/SKILL.md, line 122
r = requests.get( - skills/sciagent/pubchem-compound-search/SKILL.md, line 139
info = requests.get(f"{BASE}/compound/cid/2244/synonyms/JSON").json()["InformationList"]["Information"][0] - skills/sciagent/pubchem-compound-search/SKILL.md, line 149
r = requests.get("https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/aspirin/description/JSON") - skills/sciagent/pubchem-compound-search/SKILL.md, line 171
j = requests.get(f"{BASE}/compound/listkey/{listkey}/cids/JSON", timeout=20).json() - skills/sciagent/pubchem-compound-search/SKILL.md, line 178
init = requests.get( - skills/sciagent/pubchem-compound-search/SKILL.md, line 193
init = requests.get( - skills/sciagent/pubchem-compound-search/SKILL.md, line 209
r = requests.get(f"{BASE}/compound/cid/2244/assaysummary/JSON", timeout=30) - skills/sciagent/pubchem-compound-search/SKILL.md, line 230
sdf = requests.get(f"{BASE}/compound/cid/{cid}/SDF", timeout=15).text - skills/sciagent/pubchem-compound-search/SKILL.md, line 236
png = requests.get(f"{BASE}/compound/cid/{cid}/PNG?image_size=large", timeout=15).content - skills/sciagent/pubchem-compound-search/SKILL.md, line 296
cid = requests.get(f"{BASE}/compound/name/{quote(d)}/cids/JSON", - skills/sciagent/pubchem-compound-search/SKILL.md, line 303
r = requests.get( - skills/sciagent/pubchem-compound-search/SKILL.md, line 326
j = requests.get(f"{BASE}/compound/listkey/{listkey}/cids/JSON", - skills/sciagent/pubchem-compound-search/SKILL.md, line 333
ref_cid = requests.get( - skills/sciagent/pubchem-compound-search/SKILL.md, line 335
ref_smi = requests.get(
and 12 more places
Safer alternatives
Low-risk skills in the same category (coding) that look related. Check that one does what you need.
Install
Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.
if [ -e ~/.agents/skills/'pubchem-compound-search' ] || [ -L ~/.agents/skills/'pubchem-compound-search' ]; then echo 'A skill folder named pubchem-compound-search already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/BioTender-max/awesome-bio-agent-skills' "$d" && git -C "$d" checkout --quiet '8cbdd18837aa6296c4e77616a03b323bd69b57b1' -- 'skills/sciagent/pubchem-compound-search' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/sciagent/pubchem-compound-search' ~/.agents/skills/'pubchem-compound-search' && rm -rf "$d"; fi
Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'pubchem-compound-search' ~/.claude/skills/'pubchem-compound-search' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.
Badge for your README
The badge for BioTender-max/awesome-bio-agent-skills shows the score of its lowest-scoring skill.
[](https://zalavijaysinh.github.io/skilltrust/repos/BioTender-max/awesome-bio-agent-skills/)
Score history
| Date | Version | Score |
|---|
| 2026-11-07 | 8cbdd18 | 77 |