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Agent skill

Chembl Molecule Search

by InternScience in InternScience/scp

Search ChEMBL database for molecule information by name to retrieve bioactivity data and chemical structures.

MITAuto-check passedResearch & Science

Install Chembl Molecule Search

skills CLI
$ npx skills add InternScience/scp --skill chembl-molecule-search -a claude-code

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

GitHub CLI
$ gh skill install InternScience/scp chembl-molecule-search --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/InternScience/scp.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/chembl-molecule-search .claude/skills/chembl-molecule-search && 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/

Facts

Skill name
chembl-molecule-search
GitHub stars
169
Used in
1 other repo
Token cost
~757 tokens
SKILL.md length
52 words
Files
1
Skills in repo
73
Repo updated
First seen
Licence
MIT

At a glance

Search ChEMBL database for molecule information by name to retrieve bioactivity data and chemical structures.

  • Works in 2 steps: MCP Server Definition → ChEMBL Molecule Search Workflow
  • Tasks that involve Drug discovery and cheminformatics
  • Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md

What it does

Chembl Molecule Search is an agent skill from InternScience/scp. Search ChEMBL database for molecule information by name to retrieve bioactivity data and chemical structures.

Its SKILL.md is about 760 tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Research & Science, covering Drug discovery and cheminformatics. The licence is MIT.

When your agent uses it

  • Tasks that involve Drug discovery and cheminformatics

Example prompts

  • “/chembl-molecule-search”

Requirements

  • Python 3

Workflow steps

2 steps, taken from the step headings in SKILL.md.

  1. MCP Server Definition
  2. ChEMBL Molecule Search Workflow

What it can do on your machine

Read from SKILL.md and the folder at commit cea5398. 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

    No scripts in the folder and no shell commands in SKILL.md (its code samples are python).

    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 Molecule Search loads about 757 tokens when it runs. Until then it costs about 33 tokens; SKILL.md has 52 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~33
When it runs · the whole SKILL.md, loaded when a task matches
~757

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); files beside SKILL.md are not scanned.

SKILL.md

The full file from InternScience/scp at commit cea5398, republished under its MIT licence (© InternScience). 52 words, ~757 tokens.

Download SKILL.mdSave it as .claude/skills/chembl-molecule-search/SKILL.md (or your agent's skills folder).
name
chembl-molecule-search
description
Search ChEMBL database for molecule information by name to retrieve bioactivity data and chemical structures.
license
MIT license
metadata.skill-author
PJLab

Usage

1. MCP Server Definition
python
import asyncio
import json
from mcp.client.streamable_http import streamablehttp_client
from mcp import ClientSession

class OrigeneClient:
    """Origene-ChEMBL MCP Client"""

    def __init__(self, server_url: str, api_key: str):
        self.server_url = server_url
        self.api_key = api_key
        self.session = None

    async def connect(self):
        try:
            self.transport = streamablehttp_client(
                url=self.server_url,
                headers={"SCP-HUB-API-KEY": self.api_key}
            )
            self.read, self.write, self.get_session_id = await self.transport.__aenter__()
            self.session_ctx = ClientSession(self.read, self.write)
            self.session = await self.session_ctx.__aenter__()
            await self.session.initialize()
            return True
        except Exception as e:
            print(f"✗ connect failure: {e}")
            return False

    async def disconnect(self):
        try:
            if self.session:
                await self.session_ctx.__aexit__(None, None, None)
            if hasattr(self, 'transport'):
                await self.transport.__aexit__(None, None, None)
        except Exception as e:
            print(f"✗ disconnect error: {e}")

    def parse_result(self, result):
        if isinstance(result, dict):
            content_list = result.get("content") or []
        else:
            content_list = getattr(result, "content", []) or []
        texts = []
        for item in content_list:
            if isinstance(item, dict):
                if item.get("type") == "text":
                    texts.append(item.get("text") or "")
            else:
                if getattr(item, "type", None) == "text":
                    texts.append(getattr(item, "text", "") or "")
        return "".join(texts)
2. ChEMBL Molecule Search Workflow

Implementation:

python
## Initialize client
client = OrigeneClient(
    "https://scp.intern-ai.org.cn/api/v1/mcp/4/Origene-ChEMBL",
    "<your-api-key>"
)

if not await client.connect():
    print("connection failed")
    exit()

## Search for molecule by name
result = await client.session.call_tool(
    "get_molecule_by_name",
    arguments={
        "molecule_name": "aspirin"
    }
)

result_data = client.parse_result(result)
print(result_data)

await client.disconnect()
Tool Descriptions

Origene-ChEMBL Server:

  • get_molecule_by_name: Search ChEMBL for molecule information
    • Args:
      • molecule_name (str): Molecule name to search
    • Returns: ChEMBL molecule data including structure and bioactivity
Use Cases
  • Drug discovery research
  • Bioactivity data retrieval
  • Chemical structure lookup
  • Target-based screening

© InternScience, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

Just SKILL.md in skills/chembl-molecule-search of InternScience/scp.

Open the folder on GitHubat commit cea5398

Used in 2 other repositories

We found 2 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in InternScience/scp, which our catalogue first saw on October 7, 2026.

Compare with similar skills

Chembl Molecule Search 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 Molecule Search compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Chembl Molecule Search this skillInternScience/scp1691 repos~757Automated safety check: PassMIT
MolecodeAtomFlow-AI/MoleCode306—~1.9kAutomated safety check: PassMIT
Drug DiscoveryTommy-yw/RunbookHermes5461 repos~2.3kAutomated safety check: PassMIT
DiffDock Molecular DockingK-Dense-AI/scientific-agent-skills48k1 repos~3kAutomated safety check: NotesMIT
Biomedical Analysis Dispatchxjtulyc/MedgeClaw6171 repos~2kAutomated safety check: PassNone
Edu Chem Reactionwy51ai/edulab1.4k—~1.2kAutomated safety check: PassApache-2.0

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Categories

Questions about Chembl Molecule Search

What does Chembl Molecule Search do?

Search ChEMBL database for molecule information by name to retrieve bioactivity data and chemical structures. Chembl Molecule Search is an agent skill from InternScience/scp. Search ChEMBL database for molecule information by name to retrieve bioactivity data and chemical structures.

When should I use Chembl Molecule Search?

Chembl Molecule Search fits situations like: tasks that involve Drug discovery and cheminformatics.

How do I install Chembl Molecule Search in Claude Code?

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

How do I install Chembl Molecule Search in Codex?

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

Can I use Chembl Molecule Search 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 InternScience/scp --skill chembl-molecule-search -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-molecule-search, .gemini/skills/chembl-molecule-search, .github/skills/chembl-molecule-search and .opencode/skills/chembl-molecule-search in your project.

What does Chembl Molecule Search need to run?

SKILL.md names no scripts, command-line tools or credentials: Chembl Molecule Search is instructions for the agent only. Our summary lists: Python 3.

Does Chembl Molecule Search 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 Molecule Search 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. Review the folder before installing.

What licence does Chembl Molecule Search use?

Chembl Molecule Search is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Chembl Molecule Search use?

About 757 tokens (SKILL.md is roughly 3k 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 Molecule Search?

Skills that share tags, products or a category with Chembl Molecule Search: Molecode (AtomFlow-AI/MoleCode, 306 stars), Drug Discovery (Tommy-yw/RunbookHermes, 546 stars), DiffDock Molecular Docking (K-Dense-AI/scientific-agent-skills, 48k stars) and Biomedical Analysis Dispatch (xjtulyc/MedgeClaw, 617 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Chembl Molecule Search?

InternScience (a GitHub organization) maintains it in InternScience/scp, which has 169 GitHub stars. The repository holds 73 skills in this directory. The repository was last updated on June 3, 2026.

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