Tooluniverse Drug Drug Interaction
wu-yc/LabClaw
Comprehensive drug-drug interaction (DDI) prediction and risk assessment.
Fetch biological assays and target proteins a chemical has been tested against via PubChem.
MITAuto-check passed
Install Drug Bioactivity Assay
$ npx skills add learningmatter-mit/AtomisticSkills --skill drug-bioactivity-assay -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install learningmatter-mit/AtomisticSkills drug-bioactivity-assay --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/drug-bioactivity-assay .claude/skills/drug-bioactivity-assay && rm -rf skills-srcUse ~/.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/
Install the "drug-bioactivity-assay" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/drug-bioactivity-assay into .claude/skills/drug-bioactivity-assay/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "drug-bioactivity-assay", 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 install https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/drug-bioactivity-assayType 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.
$ npx skills add learningmatter-mit/AtomisticSkills --skill drug-bioactivity-assay -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install learningmatter-mit/AtomisticSkills drug-bioactivity-assay --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/drug-bioactivity-assay .agents/skills/drug-bioactivity-assay && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "drug-bioactivity-assay" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/drug-bioactivity-assay into .agents/skills/drug-bioactivity-assay/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "drug-bioactivity-assay", 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.
$ npx skills add learningmatter-mit/AtomisticSkills --skill drug-bioactivity-assay -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install learningmatter-mit/AtomisticSkills drug-bioactivity-assay --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/drug-bioactivity-assay .cursor/skills/drug-bioactivity-assay && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "drug-bioactivity-assay" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/drug-bioactivity-assay into .cursor/skills/drug-bioactivity-assay/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "drug-bioactivity-assay", 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 https://github.com/learningmatter-mit/AtomisticSkills.git --path skills/drug-bioactivity-assay--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add learningmatter-mit/AtomisticSkills --skill drug-bioactivity-assay -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install learningmatter-mit/AtomisticSkills drug-bioactivity-assay --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/drug-bioactivity-assay .gemini/skills/drug-bioactivity-assay && rm -rf skills-srcUse ~/.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/
Install the "drug-bioactivity-assay" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/drug-bioactivity-assay into .gemini/skills/drug-bioactivity-assay/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "drug-bioactivity-assay", 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.
$ gh skill install learningmatter-mit/AtomisticSkills drug-bioactivity-assayInstalls 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).
$ npx skills add learningmatter-mit/AtomisticSkills --skill drug-bioactivity-assay -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/drug-bioactivity-assay .github/skills/drug-bioactivity-assay && rm -rf skills-srcUse ~/.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/
Install the "drug-bioactivity-assay" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/drug-bioactivity-assay into .github/skills/drug-bioactivity-assay/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "drug-bioactivity-assay", 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.
$ npx skills add learningmatter-mit/AtomisticSkills --skill drug-bioactivity-assay -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install learningmatter-mit/AtomisticSkills drug-bioactivity-assay --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/drug-bioactivity-assay .opencode/skills/drug-bioactivity-assay && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "drug-bioactivity-assay" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/drug-bioactivity-assay into .opencode/skills/drug-bioactivity-assay/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "drug-bioactivity-assay", 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
drug-bioactivity-assay- GitHub stars
- 176
- Token cost
- ~693 tokens
- SKILL.md length
- 239 words
- Files
- 4 (incl. scripts)
- Skills in repo
- 129
- Repo updated
- First seen
- Licence
- MIT
At a glance
Fetch biological assays and target proteins a chemical has been tested against via PubChem.
- Works in 2 steps: Extract All Assays → Extract Only 'Active' Results
- SKILL.md covers Goal, Instructions, Examples and Constraints
- Runs Python scripts from its folder
What it does
Drug Bioactivity Assay is an agent skill from learningmatter-mit/AtomisticSkills. Fetch biological assays and target proteins a chemical has been tested against via PubChem.
Its SKILL.md is about 690 tokens, which your agent loads only when the skill is triggered. The skill folder holds 6 other files, including scripts (for example `examples/imatinib/README.md`, `examples/imatinib/assays_imatinib_active.json` and `scripts/get_assays.py`).
The repository describes itself as: Integrating AtomisticSkills into Agentic IDEs (Cursor, Claude Code, Codex, Google Antigravity, Hermes Agent, etc). The licence is MIT.
Example prompts
- “/drug-bioactivity-assay”
Requirements
- Python 3
Workflow steps
2 steps, taken from the step headings in SKILL.md.
What it can do on your machine
Read from SKILL.md and the folder at commit 6257444. 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 1 file in scripts/ (Python), which the agent can run.
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
github.com
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
Drug Bioactivity Assay loads about 693 tokens when it runs. Until then it costs about 29 tokens; SKILL.md has 239 words of instructions outside code blocks.
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 learningmatter-mit/AtomisticSkills at commit 6257444, republished under its MIT licence (© learningmatter-mit). 239 words, ~693 tokens.
Download SKILL.mdSave it as
.claude/skills/drug-bioactivity-assay/SKILL.md (or your agent's skills folder). This skill also uses 3 other files; get the full folder from GitHub.- name
- drug-bioactivity-assay
- description
- Fetch biological assays and target proteins a chemical has been tested against via PubChem.
- metadata.category
- drug-discovery
- metadata.venv
- cpu
Bioactivity and Assay Data Retrieval
Goal
To programmatically retrieve the testing history of a specific chemical compound against biological targets using PubChem's Assay Summary endpoint. This skill allows filtering for "Active" outcomes, providing assay IDs (AIDs), target GeneIDs, and micromolar activity values to assess a compound's promiscuity or target specificity.
Instructions
1. Extract All Assays
Retrieve all assays for a given compound (CID), regardless of outcome:
${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/scripts/get_assays.py \
--cid 2244 \
--limit 50 \
--outdir research/aspirin_assays \
--output aspirin_all_assays.json2. Extract Only 'Active' Results
Use the --active_only flag to strictly return assays where the compound was marked as "Active" or showed positive binding/inhibition.
${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/scripts/get_assays.py \
--cid 5291 \
--active_only \
--limit 50 \
--outdir research/imatinib_assays \
--output imatinib_active_assays.jsonParameters:
--cid: PubChem CID of the target molecule (e.g., 5291 for Imatinib).--outdir: Directory to save the resulting JSON file.--active_only: (Optional) Flag to strictly filter results to assays where the test outcome was "Active".--limit: (Optional) Maximum number of assays to retrieve (default: 1000) to keep JSON sizes manageable.--output: (Optional) Output filename (default:assay_summary.json).
Examples
We can test extracting known active targets for the cancer drug Imatinib (CID: 5291).
${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/scripts/get_assays.py \
--cid 5291 \
--active_only \
--limit 20 \
--outdir ${CLAUDE_SKILL_DIR}/examples/imatinib \
--output assays_imatinib_active.jsonConstraints
- Assay Availability: Compounds with no biological testing history in PubChem will return 0 results.
- Reporting Variations: High-throughput screening (HTS) assay results often lack explicit target GeneIDs or quantitative Activity Values compared to confirmatory literature assays. The script retrieves whatever is available natively in the column.
- Network Limits: PubChem can sporadically drop connections when rendering very large assay summaries. The script automatically handles connection drops and
HTTP 503blocking via exponential backoff.
Author: Bowen Deng Contact: GitHub @learningmatter-mit
© learningmatter-mit, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
SKILL.md and 3 other files (scripts) in skills/drug-bioactivity-assay of learningmatter-mit/AtomisticSkills.
- SKILL.md
- examples/imatinib/README.md
- examples/imatinib/assays_imatinib_active.json
- scripts/get_assays.py
Open the folder on GitHubat commit 6257444
Compare with similar skills
Drug Bioactivity Assay 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.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Drug Bioactivity Assay this skilllearningmatter-mit/AtomisticSkills | 176 | — | ~693 | Automated safety check: Pass | MIT | |
| Tooluniverse Drug Drug Interactionwu-yc/LabClaw | 1.1k | 2 repos | ~813 | Automated safety check: Pass | None | |
| Tooluniverse Chemical Safetywu-yc/LabClaw | 1.1k | 2 repos | ~7.5k | Automated safety check: Pass | None | |
| Chemical Structure ConverterLeoYeAI/openclaw-master-skills | 2.2k | — | ~7k | Automated safety check: Notes | MIT | |
| Chemical Structure Converteraipoch/medical-research-skills | 2k | — | ~1.7k | Automated safety check: Pass | MIT | |
| Bio Structural Biology Alphafold PredictionsFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~2.1k | Automated safety check: Pass | None |
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Questions about Drug Bioactivity Assay
What does Drug Bioactivity Assay do?
Fetch biological assays and target proteins a chemical has been tested against via PubChem. Drug Bioactivity Assay is an agent skill from learningmatter-mit/AtomisticSkills. Fetch biological assays and target proteins a chemical has been tested against via PubChem.
How do I install Drug Bioactivity Assay in Claude Code?
Run `npx skills add learningmatter-mit/AtomisticSkills --skill drug-bioactivity-assay -a claude-code`. Or copy the skill folder (skills/drug-bioactivity-assay in learningmatter-mit/AtomisticSkills) into .claude/skills/drug-bioactivity-assay in your project. Claude Code loads it when a task matches its description.
How do I install Drug Bioactivity Assay in Codex?
Run `npx skills add learningmatter-mit/AtomisticSkills --skill drug-bioactivity-assay -a codex`. Or copy the skill folder (skills/drug-bioactivity-assay in learningmatter-mit/AtomisticSkills) into .agents/skills/drug-bioactivity-assay in your project. Codex loads it when a task matches its description.
Can I use Drug Bioactivity Assay 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 learningmatter-mit/AtomisticSkills --skill drug-bioactivity-assay -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/drug-bioactivity-assay, .gemini/skills/drug-bioactivity-assay, .github/skills/drug-bioactivity-assay and .opencode/skills/drug-bioactivity-assay in your project.
What does Drug Bioactivity Assay need to run?
Going by SKILL.md and its folder, Drug Bioactivity Assay needs Python for the scripts in its folder. Our summary lists: Python 3.
Does Drug Bioactivity Assay access the network?
SKILL.md names 1 domain. As links in the text: github.com. This is read from the text; nothing was executed.
Is Drug Bioactivity Assay 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 Drug Bioactivity Assay use?
Drug Bioactivity Assay is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Drug Bioactivity Assay use?
About 693 tokens (SKILL.md is roughly 2.8k 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 Drug Bioactivity Assay?
Skills that share tags, products or a category with Drug Bioactivity Assay: Tooluniverse Drug Drug Interaction (wu-yc/LabClaw, 1.1k stars), Tooluniverse Chemical Safety (wu-yc/LabClaw, 1.1k stars), Chemical Structure Converter (LeoYeAI/openclaw-master-skills, 2.2k stars) and Chemical Structure Converter (aipoch/medical-research-skills, 2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Drug Bioactivity Assay?
learningmatter-mit (a GitHub organization) maintains it in learningmatter-mit/AtomisticSkills, which has 176 GitHub stars. The repository holds 129 skills in this directory. The repository was last updated on October 7, 2026.
Source: learningmatter-mit/AtomisticSkills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.