Agent skill

Chembl

Small-molecule drug lookup by exact drug name or ChEMBL ID. An agent skill from lamm-mit/scienceclaw.

Apache-2.0Auto-check passedResearch & Science

Install Chembl

skills CLI

$ npx skills add lamm-mit/scienceclaw --skill chembl -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI

$ gh skill install lamm-mit/scienceclaw chembl --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy

$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/chembl .claude/skills/chembl && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Paste into Claude Code

Install the "chembl" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/chembl into .claude/skills/chembl/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chembl", then confirm the skill loads.

Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

$skill-installer

$skill-installer install https://github.com/lamm-mit/scienceclaw/tree/main/skills/chembl

Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.

skills CLI

$ npx skills add lamm-mit/scienceclaw --skill chembl -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install lamm-mit/scienceclaw chembl --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/chembl .agents/skills/chembl && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "chembl" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/chembl into .agents/skills/chembl/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chembl", then confirm the skill loads.

Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add lamm-mit/scienceclaw --skill chembl -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install lamm-mit/scienceclaw chembl --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/chembl .cursor/skills/chembl && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "chembl" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/chembl into .cursor/skills/chembl/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chembl", then confirm the skill loads.

Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

gemini skills install

$ gemini skills install https://github.com/lamm-mit/scienceclaw.git --path skills/chembl

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add lamm-mit/scienceclaw --skill chembl -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install lamm-mit/scienceclaw chembl --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/chembl .gemini/skills/chembl && rm -rf skills-src

Use ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.

Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/

Paste into Gemini CLI

Install the "chembl" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/chembl into .gemini/skills/chembl/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chembl", then confirm the skill loads.

Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

GitHub CLI

$ gh skill install lamm-mit/scienceclaw chembl

Installs for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).

skills CLI

$ npx skills add lamm-mit/scienceclaw --skill chembl -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/chembl .github/skills/chembl && rm -rf skills-src

Use ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.

GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/

Paste into GitHub Copilot

Install the "chembl" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/chembl into .github/skills/chembl/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chembl", then confirm the skill loads.

GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add lamm-mit/scienceclaw --skill chembl -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install lamm-mit/scienceclaw chembl --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/chembl .opencode/skills/chembl && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "chembl" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/chembl into .opencode/skills/chembl/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "chembl", then confirm the skill loads.

OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

Facts

Skill name: chembl
GitHub stars: 244
Token cost: ~841 tokens
SKILL.md length: 319 words
Files: 3 (incl. scripts)
Skills in repo: 85
Repo updated: Aug 21, 2026
First seen: Oct 7, 2026
Licence: Apache-2.0

At a glance

Small-molecule drug lookup by exact drug name or ChEMBL ID. An agent skill from lamm-mit/scienceclaw.

Works in 3 steps: Search PubMed first with the mechanism… → Extract specific small-molecule compound… → Then query ChEMBL with those specific…
Tasks that involve Academic paper search
SKILL.md covers IMPORTANT: Query must be a…, When NOT to Use This Skill, Overview and Usage, plus 3 more sections
Runs Python scripts from its folder; calls python3

What it does

Chembl is an agent skill from lamm-mit/scienceclaw. Small-molecule drug lookup by exact drug name or ChEMBL ID. Query MUST be a single drug name or ID — 1 to 3 words maximum. Valid examples: 'sotorasib', 'imatinib', 'ibrutinib', 'CHEMBL25', 'AMG 510'. If the topic is 'sotorasib KRAS G12C', the correct query is 'sotorasib'. If the topic is 'BTK inhibitors in CLL', search PubMed first to get a specific drug name, then query ChEMBL with that name. Strip protein names, mutation labels, and mechanism words — pass only the compound name.

Its SKILL.md is about 840 tokens, which your agent loads only when the skill is triggered. The skill folder holds 4 other files, including scripts (for example `scripts/chembl_search.py`).

It sits in Research & Science, covering Academic paper search and Drug discovery and cheminformatics. It works with PubMed. The licence is Apache-2.0.

When your agent uses it

Tasks that involve Academic paper search
Tasks that involve Drug discovery and cheminformatics

Example prompts

“sotorasib”
“imatinib”
“ibrutinib”
“/chembl”

Requirements

Python 3

Workflow steps

3 steps, taken from the first numbered list in SKILL.md.

Search PubMed first with the mechanism query
Extract specific small-molecule compound names from the papers (e.g. "ARV-110", "dBET6", "MZ1")
Then query ChEMBL with those specific names

What it can do on your machine

Read from SKILL.md and the folder at commit ab9aba1. It shows what the files ask for, not the result of running them.

Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Ships 2 files in scripts/ (Python), which the agent can run.
Shell commands in SKILL.md call:
- python3
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Chembl loads about 841 tokens when it runs. Until then it costs about 123 tokens; SKILL.md has 319 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~123
When it runs · the whole SKILL.md, loaded when a task matches: ~841

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.

SKILL.md

The full file from lamm-mit/scienceclaw at commit ab9aba1, republished under its Apache-2.0 licence (© lamm-mit). 319 words, ~841 tokens.

Download SKILL.mdSave it as .claude/skills/chembl/SKILL.md (or your agent's skills folder). This skill also uses 2 other files; get the full folder from GitHub.

name: chembl
description: Small-molecule drug lookup by exact drug name or ChEMBL ID. Query MUST be a single drug name or ID — 1 to 3 words maximum. Valid examples: 'sotorasib', 'imatinib', 'ibrutinib', 'CHEMBL25', 'AMG 510'. If the topic is 'sotorasib KRAS G12C', the correct query is 'sotorasib'. If the topic is 'BTK inhibitors in CLL', search PubMed first to get a specific drug name, then query ChEMBL with that name. Strip protein names, mutation labels, and mechanism words — pass only the compound name.

ChEMBL Drug and Compound Lookup

Query the ChEMBL database for drug-like molecules, drug targets, and bioactivity data. ChEMBL is EBI's open database of drug discovery and medicinal chemistry.

IMPORTANT: Query must be a specific drug or compound name

ChEMBL searches by molecule name. Always use a specific drug name or compound identifier (e.g. sotorasib, ibrutinib, CHEMBL1873475). Do NOT pass topic phrases like "kinase inhibitor resistance" — these will return garbage results. If the topic mentions multiple drugs, pick the most specific one.

When NOT to Use This Skill

Do NOT use ChEMBL when the query is any of the following — it will return large biologics, cell therapy entries, or protein records with MW=?, logP=?, phase=-1:

Biological therapies: cell therapies, stem cells, antibodies, CAR-T, biologics (e.g. "allogeneic mesenchymal stem cells", "anti-PD1 antibody")
Mechanism or concept phrases: "proximity-induced degradation", "PROTAC linker", "covalent warhead", "undruggable target"
Disease names without a specific drug: "Alzheimer's disease", "pancreatic cancer", "KRAS oncogenesis"
Pathway or process terms: "mTOR signaling", "ubiquitin-proteasome pathway", "kinase cascade"

Correct workflow for mechanism-based topics (e.g. PROTAC, degrader, proximity):

Search PubMed first with the mechanism query
Extract specific small-molecule compound names from the papers (e.g. "ARV-110", "dBET6", "MZ1")
Then query ChEMBL with those specific names

Overview

Search molecules by name or ChEMBL ID
Retrieve molecular properties, SMILES, drug indications
Find targets and bioactivity (IC50, Ki, etc.)
No API key required

Usage

Search by compound or drug name

bash

python3 {baseDir}/scripts/chembl_search.py --query "aspirin"

Get molecule by ChEMBL ID

bash

python3 {baseDir}/scripts/chembl_search.py --chembl-id CHEMBL25

Detailed output

bash

python3 {baseDir}/scripts/chembl_search.py --query "imatinib" --format detailed

Limit search results

bash

python3 {baseDir}/scripts/chembl_search.py --query "kinase inhibitor" --max-results 5

Parameters

Parameter	Description	Default
`--query`	Compound or drug name or search term	-
`--chembl-id`	ChEMBL molecule ID (e.g. CHEMBL25)	-
`--max-results`	Max results for search	10
`--format`	Output: summary, detailed, json	summary

Output

Summary: ChEMBL ID, pref_name, molecular formula, MW, SMILES, max_phase
Detailed: Adds drug type, first approval, indications, targets
JSON: Full API response

Notes

ChEMBL IDs look like CHEMBL25, CHEMBL1234567
Use --query for name or text search
Use --chembl-id when you know the exact molecule ID

Files

SKILL.md and 2 other files (scripts) in skills/chembl of lamm-mit/scienceclaw.

SKILL.md
scripts/__pycache__/chembl_search.cpython-313.pyc
scripts/chembl_search.py

Open the folder on GitHubat commit ab9aba1

Compare with similar skills

Chembl next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Chembl compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Chembl this skilllamm-mit/scienceclaw	244	—	~841	Automated safety check: Pass	Apache-2.0	1 mo ago
Literature Reviewneflibata-feng/MyArxiv-Agent	126	21 repos	~5.9k	Automated safety check: Notes	MIT	yesterday
Citation ManagementK-Dense-AI/claude-scientific-writer	2.4k	3 repos	~3.9k	Automated safety check: Notes	MIT	8 days ago
Citation Managementneflibata-feng/MyArxiv-Agent	126	20 repos	~8.1k	Automated safety check: Notes	MIT	yesterday
Paper Searchopenags/paper-search-mcp	2.8k	—	~1.2k	Automated safety check: Notes	MIT	6 days ago
Rival Search MCPdamionrashford/RivalSearchMCP	132	1 repos	~796	Automated safety check: Pass	MIT	today

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Questions about Chembl

What does Chembl do?

Small-molecule drug lookup by exact drug name or ChEMBL ID. An agent skill from lamm-mit/scienceclaw. Chembl is an agent skill from lamm-mit/scienceclaw. Small-molecule drug lookup by exact drug name or ChEMBL ID.

When should I use Chembl?

Chembl fits situations like: tasks that involve Academic paper search; tasks that involve Drug discovery and cheminformatics.

How do I install Chembl in Claude Code?

Run `npx skills add lamm-mit/scienceclaw --skill chembl -a claude-code`. Or copy the skill folder (skills/chembl in lamm-mit/scienceclaw) into .claude/skills/chembl in your project. Claude Code loads it when a task matches its description.

How do I install Chembl in Codex?

Run `npx skills add lamm-mit/scienceclaw --skill chembl -a codex`. Or copy the skill folder (skills/chembl in lamm-mit/scienceclaw) into .agents/skills/chembl in your project. Codex loads it when a task matches its description.

Can I use Chembl in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add lamm-mit/scienceclaw --skill chembl -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/chembl, .gemini/skills/chembl, .github/skills/chembl and .opencode/skills/chembl in your project.

What does Chembl need to run?

Going by SKILL.md and its folder, Chembl needs Python for the scripts in its folder and the command-line tools its instructions call (python3). Our summary lists: Python 3.

Does Chembl access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Chembl safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does Chembl use?

Chembl is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Chembl use?

About 841 tokens (SKILL.md is roughly 3.4k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Chembl?

Skills that share tags, products or a category with Chembl: Literature Review (neflibata-feng/MyArxiv-Agent, 126 stars), Citation Management (K-Dense-AI/claude-scientific-writer, 2.4k stars), Citation Management (neflibata-feng/MyArxiv-Agent, 126 stars) and Paper Search (openags/paper-search-mcp, 2.8k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Chembl?

lamm-mit (a GitHub user) maintains it in lamm-mit/scienceclaw, which has 244 GitHub stars. The repository holds 85 skills in this directory. The repository was last updated on August 21, 2026.

Source: lamm-mit/scienceclaw on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Install Chembl

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

Workflow steps

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

ChEMBL Drug and Compound Lookup

IMPORTANT: Query must be a specific drug or compound name

When NOT to Use This Skill

Overview

Usage

Search by compound or drug name

Get molecule by ChEMBL ID

Detailed output

Limit search results

Parameters

Output

Notes

Files

Compare with similar skills

Similar skills

More from lamm-mit/scienceclaw

Related

Questions about Chembl