Agent skill

Patsnap Chemical Molecular

Patsnap Chemical Molecular MCP for AI agents. An agent skill from patsnap/mcp.

Apache-2.0Auto-check passedLegal & Compliance

Install Patsnap Chemical Molecular

skills CLI

$ npx skills add patsnap/mcp --skill patsnap-chemical-molecular -a claude-code

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

GitHub CLI

$ gh skill install patsnap/mcp patsnap-chemical-molecular --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/patsnap/mcp.git skills-src && mkdir -p .claude/skills && cp -r skills-src/life-sciences/patsnap-chemical-molecular .claude/skills/patsnap-chemical-molecular && 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 "patsnap-chemical-molecular" agent skill from https://github.com/patsnap/mcp/tree/main/life-sciences/patsnap-chemical-molecular into .claude/skills/patsnap-chemical-molecular/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "patsnap-chemical-molecular", 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/patsnap/mcp/tree/main/life-sciences/patsnap-chemical-molecular

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 patsnap/mcp --skill patsnap-chemical-molecular -a codex

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

GitHub CLI

$ gh skill install patsnap/mcp patsnap-chemical-molecular --agent codex

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

Manual copy

$ git clone --depth 1 https://github.com/patsnap/mcp.git skills-src && mkdir -p .agents/skills && cp -r skills-src/life-sciences/patsnap-chemical-molecular .agents/skills/patsnap-chemical-molecular && 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 "patsnap-chemical-molecular" agent skill from https://github.com/patsnap/mcp/tree/main/life-sciences/patsnap-chemical-molecular into .agents/skills/patsnap-chemical-molecular/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "patsnap-chemical-molecular", 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 patsnap/mcp --skill patsnap-chemical-molecular -a cursor

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

GitHub CLI

$ gh skill install patsnap/mcp patsnap-chemical-molecular --agent cursor

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

Manual copy

$ git clone --depth 1 https://github.com/patsnap/mcp.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/life-sciences/patsnap-chemical-molecular .cursor/skills/patsnap-chemical-molecular && 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 "patsnap-chemical-molecular" agent skill from https://github.com/patsnap/mcp/tree/main/life-sciences/patsnap-chemical-molecular into .cursor/skills/patsnap-chemical-molecular/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "patsnap-chemical-molecular", 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/patsnap/mcp.git --path life-sciences/patsnap-chemical-molecular

--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 patsnap/mcp --skill patsnap-chemical-molecular -a gemini-cli

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

GitHub CLI

$ gh skill install patsnap/mcp patsnap-chemical-molecular --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/patsnap/mcp.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/life-sciences/patsnap-chemical-molecular .gemini/skills/patsnap-chemical-molecular && 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 "patsnap-chemical-molecular" agent skill from https://github.com/patsnap/mcp/tree/main/life-sciences/patsnap-chemical-molecular into .gemini/skills/patsnap-chemical-molecular/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "patsnap-chemical-molecular", 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 patsnap/mcp patsnap-chemical-molecular

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 patsnap/mcp --skill patsnap-chemical-molecular -a github-copilot

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

Manual copy

$ git clone --depth 1 https://github.com/patsnap/mcp.git skills-src && mkdir -p .github/skills && cp -r skills-src/life-sciences/patsnap-chemical-molecular .github/skills/patsnap-chemical-molecular && 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 "patsnap-chemical-molecular" agent skill from https://github.com/patsnap/mcp/tree/main/life-sciences/patsnap-chemical-molecular into .github/skills/patsnap-chemical-molecular/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "patsnap-chemical-molecular", 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 patsnap/mcp --skill patsnap-chemical-molecular -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 patsnap/mcp patsnap-chemical-molecular --agent opencode

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

Manual copy

$ git clone --depth 1 https://github.com/patsnap/mcp.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/life-sciences/patsnap-chemical-molecular .opencode/skills/patsnap-chemical-molecular && 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 "patsnap-chemical-molecular" agent skill from https://github.com/patsnap/mcp/tree/main/life-sciences/patsnap-chemical-molecular into .opencode/skills/patsnap-chemical-molecular/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "patsnap-chemical-molecular", 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: patsnap-chemical-molecular
GitHub stars: 113
Token cost: ~779 tokens
SKILL.md length: 285 words
Files: 2
Skills in repo: 32
Repo updated: Aug 20, 2026
First seen: Oct 7, 2026
Licence: Apache-2.0

At a glance

Patsnap Chemical Molecular MCP for AI agents. An agent skill from patsnap/mcp.

Works in 4 steps: Chemical Entity Recognition → Structure-Based Search → Bioactivity & Property Analysis → …
Tasks that involve Intellectual property
SKILL.md covers Setup, Prerequisites, Instructions for AI Agents and Example Workflows, plus 1 more section
Reaches connect.patsnap.com

What it does

Patsnap Chemical Molecular is an agent skill from patsnap/mcp. Patsnap Chemical Molecular MCP for AI agents. Search 160M+ chemical structures, synthetic routes, and bioactivity data via specialized chemistry tools.

Its SKILL.md is about 780 tokens, which your agent loads only when the skill is triggered. The skill folder holds 1 other file (for example `README.md`).

It sits in Legal & Compliance, covering Intellectual property, MCP servers and Drug discovery and cheminformatics. It works with Model Context Protocol. The repository describes itself as: MCP server for 200M+ patents, scientific literature, chemistry and pharma records. Search prior art and R&D intelligence powered by PatSnap's proprietary databases via Claude… The licence is Apache-2.0.

When your agent uses it

Tasks that involve Intellectual property
Tasks that involve MCP servers
Tasks that involve Drug discovery and cheminformatics

Example prompts

“/patsnap-chemical-molecular”

Requirements

A credential in YOUR_API_KEY

Workflow steps

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

Chemical Entity Recognition
Structure-Based Search
Bioactivity & Property Analysis
Output Synthesis

What it can do on your machine

Read from SKILL.md and the folder at commit 7a4b429. 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 json).
From the folder's file list and the shell code blocks in SKILL.md.
Network
Hosts in commands or code, which the agent is likely to contact:
- connect.patsnap.com
Also links to:
- open.patsnap.com
- eureka.patsnap.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

Patsnap Chemical Molecular loads about 779 tokens when it runs. Until then it costs about 45 tokens; SKILL.md has 285 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~45
When it runs · the whole SKILL.md, loaded when a task matches: ~779

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 patsnap/mcp at commit 7a4b429, republished under its Apache-2.0 licence (© patsnap). 285 words, ~779 tokens.

Download SKILL.mdSave it as .claude/skills/patsnap-chemical-molecular/SKILL.md (or your agent's skills folder). This skill also uses 1 other file; get the full folder from GitHub.

name: patsnap-chemical-molecular
description: Patsnap Chemical Molecular MCP for AI agents. Search 160M+ chemical structures, synthetic routes, and bioactivity data via specialized chemistry tools.
homepage: https://open.patsnap.com/marketplace/mcp-servers/chemical-molecular
metadata.author: Patsnap
metadata.category: Life Science
metadata.version: 1.0.0

Setup

Get your API Key at https://open.patsnap.com

Patsnap Chemical Molecular

This skill connects your AI agent to Patsnap's Chemical Molecular MCP server — providing professional-grade chemistry search and analysis capabilities.

With this skill, your agent can navigate the complex world of small molecules, from structure-based patent searching to bioactivity data retrieval and synthetic route analysis.

Prerequisites

This skill requires the Patsnap Chemical Intelligence MCP server to be configured in your environment:

json

{
  "mcpServers": {
    "chemical_molecular": {
      "url": "https://connect.patsnap.com/713886/logic-mcp?apikey=YOUR_API_KEY",
      "type": "streamableHttp"
    }
  }
}

Get your API key at open.patsnap.com.

For the full list of available tools and input parameters, refer to the official MCP server documentation: https://open.patsnap.com/marketplace/mcp-servers/chemical-molecular

Instructions for AI Agents

Step 1: Chemical Entity Recognition

When a user mentions a chemical name, drug, or SMILES string, use the chemical normalization tools to resolve the entity to a standard structure or Patsnap internal ID.

Step 2: Structure-Based Search

Use Substructure Search to find molecules containing a specific scaffold.
Use Similarity Search to find analogs of a lead compound.
Combine structure search with patent filters to investigate the chemical IP landscape.

Step 3: Bioactivity & Property Analysis

Retrieve IC50, Ki, and other bioactivity data from literature and patents to evaluate compound potency and selectivity.

Step 4: Output Synthesis

Present chemical data with:

SMILES/InChI strings for precise identification.
Visual descriptions of scaffolds and functional groups.
Tabular comparisons of bioactivity across different analogs.

Example Workflows

Lead Optimization Support

Identify lead compound structure.
Run similarity search to find known analogs.
Retrieve bioactivity data for all analogs to identify SAR (Structure-Activity Relationship) trends.

Chemical IP Clearance

Input a candidate molecule structure.
Run substructure search across global patent databases.
Identify key patents that may cover the candidate scaffold.

Resources

Patsnap Life Sciences: eureka.patsnap.com/ls-landing
MCP Server: open.patsnap.com/marketplace/mcp-servers
API Docs: open.patsnap.com/devportal

Files

SKILL.md and 1 other file in life-sciences/patsnap-chemical-molecular of patsnap/mcp.

SKILL.md
README.md

Open the folder on GitHubat commit 7a4b429

Compare with similar skills

Patsnap Chemical Molecular 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.

Patsnap Chemical Molecular compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Patsnap Chemical Molecular this skillpatsnap/mcp	113	—	~779	Automated safety check: Pass	Apache-2.0	1 mo ago
Chemgraphargonne-lcf/ChemGraph	162	—	~2.7k	Automated safety check: Pass	Apache-2.0	yesterday
Development AssistantRobThePCGuy/Claude-Patent-Creator	196	—	~1.3k	Automated safety check: Notes	MIT	4 days ago
Aminer MCP ResearchDrchronx/ai-agent-research-starter-kit	139	—	~1.1k	Automated safety check: Pass	Custom licence	4 mo ago
Tw Legal RAGaa0101181514/tw-legal-rag	328	—	~580	Automated safety check: Pass	Custom licence	today
Hcls Build Agentaws-samples/amazon-bedrock-agents-healthcare-lifesciences	274	—	~885	Automated safety check: Pass	MIT-0	9 days ago

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Questions about Patsnap Chemical Molecular

What does Patsnap Chemical Molecular do?

Patsnap Chemical Molecular MCP for AI agents. An agent skill from patsnap/mcp. Patsnap Chemical Molecular is an agent skill from patsnap/mcp. Patsnap Chemical Molecular MCP for AI agents.

When should I use Patsnap Chemical Molecular?

Patsnap Chemical Molecular fits situations like: tasks that involve Intellectual property; tasks that involve MCP servers; tasks that involve Drug discovery and cheminformatics.

How do I install Patsnap Chemical Molecular in Claude Code?

Run `npx skills add patsnap/mcp --skill patsnap-chemical-molecular -a claude-code`. Or copy the skill folder (life-sciences/patsnap-chemical-molecular in patsnap/mcp) into .claude/skills/patsnap-chemical-molecular in your project. Claude Code loads it when a task matches its description.

How do I install Patsnap Chemical Molecular in Codex?

Run `npx skills add patsnap/mcp --skill patsnap-chemical-molecular -a codex`. Or copy the skill folder (life-sciences/patsnap-chemical-molecular in patsnap/mcp) into .agents/skills/patsnap-chemical-molecular in your project. Codex loads it when a task matches its description.

Can I use Patsnap Chemical Molecular 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 patsnap/mcp --skill patsnap-chemical-molecular -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/patsnap-chemical-molecular, .gemini/skills/patsnap-chemical-molecular, .github/skills/patsnap-chemical-molecular and .opencode/skills/patsnap-chemical-molecular in your project.

What does Patsnap Chemical Molecular need to run?

SKILL.md names no scripts, command-line tools or credentials: Patsnap Chemical Molecular is instructions for the agent only. Our summary lists: A credential in YOUR_API_KEY.

Does Patsnap Chemical Molecular access the network?

SKILL.md names 3 domains. In commands or code: connect.patsnap.com; the agent is likely to contact it when it follows the instructions. As links in the text: open.patsnap.com and eureka.patsnap.com. This is read from the text; nothing was executed.

Is Patsnap Chemical Molecular 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 Patsnap Chemical Molecular use?

Patsnap Chemical Molecular 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 Patsnap Chemical Molecular use?

About 779 tokens (SKILL.md is roughly 3.1k 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 Patsnap Chemical Molecular?

Skills that share tags, products or a category with Patsnap Chemical Molecular: Chemgraph (argonne-lcf/ChemGraph, 162 stars), Development Assistant (RobThePCGuy/Claude-Patent-Creator, 196 stars), Aminer MCP Research (Drchronx/ai-agent-research-starter-kit, 139 stars) and Tw Legal RAG (aa0101181514/tw-legal-rag, 328 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Patsnap Chemical Molecular?

patsnap (a GitHub organization) maintains it in patsnap/mcp, which has 113 GitHub stars. The repository holds 32 skills in this directory. The repository was last updated on August 20, 2026.

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

Install Patsnap Chemical Molecular

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

Setup

Patsnap Chemical Molecular

Prerequisites

Instructions for AI Agents

Step 1: Chemical Entity Recognition

Step 2: Structure-Based Search

Step 3: Bioactivity & Property Analysis

Step 4: Output Synthesis

Example Workflows

Lead Optimization Support

Chemical IP Clearance

Resources

Files

Compare with similar skills

Similar skills

More from patsnap/mcp

Related

Questions about Patsnap Chemical Molecular