Pubchem MCP Server

Name: Pubchem MCP Server
Author: cyanheads

作者：cyanheads版本 0.8.0i★ –i电脑或云端

注册名称io.github.cyanheads/pubchem-mcp-server

安装

概览

作者提供的说明（英文原文）

Search PubChem compounds, properties, safety data, bioactivity, and cross-references.

PopNx MCP 的三大支柱

这三项永远不会合并成一个分数：意见、测量和人气是不同的东西。

用户评价i暂无评价评价功能将在后续阶段与账户功能一起开放
我们的基础检查i3 项中通过 3 项依据公开信息检查；尚未扫描代码
使用情况i非常新↓ 310/周 · ★ –

它能帮你做什么

我们还没有为它写通俗的介绍。下面是我们从注册中心读取到的事实。

连接方式: 电脑或云端
传输方式: stdio, Streamable HTTP
分类: 搜索与 AI 记忆

安装

选择你使用的 AI 应用，然后复制设置。

安装之前

基础检查：3 项中通过 3 项
在作者的服务器上运行：你向它提出的内容会经过他们的服务器。
可以做 10 件事（工具） pubchem_search_compounds, pubchem_get_compound_details, pubchem_get_compound_image, pubchem_get_compound_3d_structure …
需要你自己填写： MCP_LOG_LEVEL

你需要

在云端运行无需安装任何东西，通过互联网连接
npm已安装 Node.js（用于 npx 命令）

你用的是哪个应用？

ClaudeClaude CodeCursorVS CodeChatGPT

在上方选择你的应用。我们会记住它，下次按钮会显示“安装到 …”。

适用于网页版、桌面版和手机版 Claude：

打开 Settings → Connectors
点击 Add custom connector
粘贴下面的地址，然后点击 Add
如果要求登录，请登录作者的服务

https://pubchem.caseyjhand.com/mcp

或者在你的电脑上运行

打开 Claude Desktop → Settings → Developer → Edit Config，把下面的内容粘贴到 claude_desktop_config.json

{
  "mcpServers": {
    "pubchem": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/pubchem-mcp-server"
      ],
      "env": {
        "MCP_LOG_LEVEL": "your-value"
      }
    }
  }
}

在终端中运行这条命令

claude mcp add --transport http pubchem https://pubchem.caseyjhand.com/mcp

或者在你的电脑上运行

claude mcp add pubchem --env MCP_LOG_LEVEL=your-value -- npx -y @cyanheads/pubchem-mcp-server

运行前请先填写空着的值。

在 Cursor 中打开

或者自己复制设置

粘贴到项目中的 .cursor/mcp.json，或 ~/.cursor/mcp.json

{
  "mcpServers": {
    "pubchem": {
      "url": "https://pubchem.caseyjhand.com/mcp"
    }
  }
}

或者在你的电脑上运行

在 Cursor 中打开

或者自己复制设置

粘贴到项目中的 .cursor/mcp.json，或 ~/.cursor/mcp.json

{
  "mcpServers": {
    "pubchem": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/pubchem-mcp-server"
      ],
      "env": {
        "MCP_LOG_LEVEL": "your-value"
      }
    }
  }
}

浏览器会先询问是否打开应用，然后应用会显示设置并请你确认。密钥的值会留空，由你自己填写。

在 VS Code 中打开

或者自己复制设置

粘贴到项目中的 .vscode/mcp.json

{
  "servers": {
    "pubchem": {
      "type": "http",
      "url": "https://pubchem.caseyjhand.com/mcp"
    }
  }
}

或者在你的电脑上运行

在 VS Code 中打开

或者自己复制设置

粘贴到项目中的 .vscode/mcp.json

{
  "servers": {
    "pubchem": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/pubchem-mcp-server"
      ],
      "env": {
        "MCP_LOG_LEVEL": "your-value"
      }
    }
  }
}

浏览器会先询问是否打开应用，然后应用会显示设置并请你确认。密钥的值会留空，由你自己填写。

ChatGPT 只能连接互联网上的服务器：

打开网页版 ChatGPT → Settings → Connectors (Apps)
点击 Create 或 Add（部分套餐需要先在 Advanced 中开启 Developer mode）
粘贴下面的地址，起个名字，然后保存
如果要求登录，请登录作者的服务

https://pubchem.caseyjhand.com/mcp

菜单名称可能因套餐和版本不同而略有差异。

你的选择通过 Cookie 保存在这台设备上，无需账户。

需要你填写的值

MCP_LOG_LEVEL env
Sets the minimum log level for output (e.g., 'debug', 'info', 'warn').

这些设置是根据作者在注册中心的条目生成的。如果 README 的写法不同，请以 README 为准。

它能做什么

工具名称和描述与服务器在 2026年11月7日报告的完全一致。这些内容由作者撰写，不是我们写的；我们以纯文本形式显示。

pubchem_search_compounds
Search PubChem for chemical compounds by identifier (name, SMILES, InChI, or InChIKey, up to 25 per call), molecular formula in Hill notation, substructure or superstructure containment, 2D Tanimoto similarity, or the compounds a bioassay (AID) found active or tested. Returns a p
pubchem_get_compound_details
Get detailed compound information by CID. Returns physicochemical properties (molecular weight, SMILES, InChIKey, XLogP, TPSA, etc.), optionally with a textual description (pharmacology, mechanism, therapeutic use), known synonyms, drug-likeness assessment (Lipinski/Veber rules),
pubchem_get_compound_image
Fetch a 2D structure diagram (PNG image) for a compound by CID.
pubchem_get_compound_3d_structure
Get a compound's default 3D conformer — atomic coordinates and bonds — for one CID. format="json" (default) returns atoms and bonds parsed into structured fields; format="sdf" returns the raw V2000 SDF text for passthrough to docking, rendering, or conformer tools. Optionally lis
pubchem_get_compound_xrefs
Get external database cross-references for a compound: PubMed citations, patent IDs, gene associations, CAS and EC numbers with the number of source records that deposited each, other registry numbers, and taxonomy IDs. Results are paged per type — capped at maxPerType with the t
pubchem_get_compound_safety
Get GHS (Globally Harmonized System) hazard classification and safety data for one or more compounds by CID. Returns signal word, pictograms, hazard statements (H-codes), and precautionary statements (P-codes) per compound, merged across sources, plus each source's own classifica
pubchem_get_bioactivity
Get a compound's bioactivity profile: which assays tested it, activity outcomes (Active/Inactive/Inconclusive), target identifiers (NCBI Gene ID, UniProt/GenBank accession), quantitative values (IC50, EC50, Ki, etc.), each assay's type (confirmatory, screening, summary, other), a
pubchem_get_compound_interactions
Get a compound's interaction data: drug-food interactions, and the molecular targets its bioassays name — one entry per target as kinds defines it, with its assay counts by outcome and most potent active value, Active targets first, most potent first. Each entry carries its origi
pubchem_search_assays
Find PubChem bioassays associated with a biological target. Search by gene symbol (e.g. "EGFR"), protein name, NCBI Gene ID, or UniProt accession. Returns a page of assay IDs (AIDs) — page past maxResults with offset — which can be explored further with pubchem_get_summary.
pubchem_get_summary
Get descriptive summaries for PubChem entities by ID. Supports assays (AID), genes (Gene ID), proteins (UniProt accession), and taxonomy (Tax ID). Up to 10 per call; identifiers past that are returned in unprocessed for a follow-up call.

基础检查i

我们检查的是任何人都能看到的信息；我们没有阅读代码。不适用的检查项不计入总数。 · 检查于 2026年11月10日

✓ 通过
作者与仓库一致
注册名称已通过 GitHub 账户 cyanheads 验证，该账户拥有此仓库
… 尚未检查
仍在维护
我们还没有从 GitHub 读取这个仓库
… 尚未检查
有许可证
我们还没有从 GitHub 读取这个仓库
✓ 通过
端点有响应
在 223 毫秒内响应（HTTP 200）
– 不适用
使用 OAuth 登录
无需登录
✓ 通过
工具描述中没有隐藏指令
已读取 10 个工具描述，未发现针对 AI 的隐藏指令

与“搜索与 AI 记忆”中的其他服务器比较i

星标数多于此分类中其他 5825 个服务器的 0%
发布到注册中心的时间比此分类中其他 5825 个服务器的 75% 更新
基础检查结果等于或优于此分类中其他 5825 个服务器的 100%

与注册中心里这个分类中所有活跃的服务器比较。只有当发布者拥有该仓库时，星标数才计入。

常见问题

Pubchem MCP Server 安全吗？

它在 3 项适用的基础检查中通过了 3 项。我们没有阅读代码。在添加密钥或令牌之前，请先看看这个服务器要求哪些权限，并使用只具备所需权限的密钥。

它需要哪些密钥或代码？

注册中心没有列出必需的密钥，不过有些服务器会在首次使用时要求你登录。

它在我的电脑上运行还是在云端？

两种方式都可以：安装在你的电脑上，或者连接云端版本。

它还在维护吗？

GitHub 仓库最后更新于–，最新版本（0.8.0）于12天前进入注册中心。

哪些应用可以使用它？

支持 MCP 的应用，例如 Claude Desktop、Claude Code、Cursor 和 VS Code。它通过 URL 连接，所以接受远程 MCP 服务器的应用也可以使用，例如开启开发者模式的 ChatGPT。

有什么可以替代它？

同一分类中有：Context7, Codebase Memory, Exa

替代选择

同一分类中其他作者的服务器，按星标数排序。

如何看卡片：↓ 每周下载量i★ GitHub 星标i三大支柱：评价 · 检查 · 使用情况i更新 = 最新版本发布到注册中心的时间i

Context7

Up-to-date docs for AI agents

作者：upstash广泛使用↓ 97.3万/周★ 6.4万今天更新

电脑或云端

安装

Codebase Memory

Codebase knowledge graph for AI agents — 162 languages, sub-ms queries, 99% fewer tokens.

作者：DeusData广泛使用↓ 1.8万/周★ 4.8万23天前更新

在你的电脑上运行

安装

Exa

Connect AI agents to Exa for web search, content fetching, and multi-step research.

作者：exa-labs广泛使用★ 52132个月前更新

在云端运行✓ exa.ai

安装

作者的 README

打开 README

按原文从作者的仓库复制。PopNx MCP 没有审查或背书其内容。HTML、图片和脚本已被移除。链接会离开本站。

@cyanheads/pubchem-mcp-server Search the PubChem chemical database for compounds, properties, safety data, bioactivity, cross-references, and entity summaries via MCP. STDIO or Streamable HTTP. 10 Tools • 6 Resources • 1 Skill

Public Hosted Server: https://pubchem.caseyjhand.com/mcp

Overview

Chemical compounds and bioassays from PubChem. Search compounds by name, formula, or structure; fetch properties, safety data, bioactivity, drug-food interactions, molecular targets, and 3D structures; and find bioassays by biological target.

Tools

Tool	Description
`pubchem_search_compounds`	Search for compounds by name, SMILES, InChI, InChIKey, formula, substructure, superstructure, or 2D similarity, or list the compounds a bioassay found active.
`pubchem_get_compound_details`	Get physicochemical properties, descriptions, synonyms, drug-likeness, and classification for compounds by CID.
`pubchem_get_compound_image`	Fetch a 2D structure diagram (PNG) for a compound by CID.
`pubchem_get_compound_3d_structure`	Fetch a 3D conformer (atomic coordinates and bonds) for a compound by CID, as parsed JSON or raw SDF.
`pubchem_get_compound_xrefs`	Get external database cross-references (PubMed, patents, genes, CAS and EC numbers, etc.).
`pubchem_get_compound_safety`	Get GHS hazard classification and safety data for one or more compounds by CID (batch).
`pubchem_get_bioactivity`	Get a compound's bioactivity profile: assay results, targets, activity values, assay types, and cited PubMed IDs; filter by outcome, molecular target, or assay type.
`pubchem_get_compound_interactions`	Get a compound's drug-food interactions and the molecular targets its assays name, each with assay counts and the most potent active value.
`pubchem_search_assays`	Find bioassays by biological target (gene symbol, protein, Gene ID, UniProt accession).
`pubchem_get_summary`	Get summaries for PubChem entities: assays, genes, proteins, taxonomy.

Resources

Compound and assay records are also exposed as URI-templated resources, backed by the same client methods as the tools; many MCP clients are tool-only and never surface resources.

Resource	Description
`pubchem://compound/{cid}`	Core physicochemical properties (JSON).
`pubchem://compound/{cid}/safety`	GHS hazard classification (JSON).
`pubchem://compound/{cid}/image`	2D structure diagram (PNG).
`pubchem://compound/{cid}/xrefs`	External cross-references (JSON).
`pubchem://compound/{cid}/bioactivity`	Bioassay activity profile (JSON).
`pubchem://assay/{aid}`	BioAssay summary (JSON).

Skills

The server publishes an agent skill, pubchem-guide, covering gates and identifier chains the tool descriptions don't carry: salt vs parent CIDs, where Gene IDs and accessions come from, why gene-symbol, Gene ID, and accession searches disagree, and how to read activity labels, potency values, and GHS data. Plugin installs (Claude Code, Codex) and the .mcpb bundle pick it up from skills/, and the server also serves it over MCP as skill://pubchem-guide/SKILL.md.

Capability reference

`pubchem_search_compounds` tool

Six search strategies: identifier (identifierType + identifiers; name/SMILES/InChI/InChIKey, 25 per call, the rest returned in unprocessed), formula (formula, Hill notation, optional allowOtherElements), substructure/superstructure and 2D similarity (query + queryType; similarity threshold 70-100, default 90), or assay (aid; compounds the bioassay marked active, or every compound tested with activeOnly: false)
Up to 200 CIDs per page (default 20; a larger maxResults is served at 200 and reported in cappedInputs); offset pages identifier and assay searches to the end of their matches, and formula, substructure, superstructure, and similarity searches to 10,000 (deeper fails with offset_ceiling_exceeded). Optional properties saves a follow-up pubchem_get_compound_details call
Reports totalFound, or a totalFoundAtLeast floor when an upstream search saturated, and unresolvedIdentifiers for inputs with no CID. Fails with aid_not_found for an unknown AID and search_query_rejected (with a hint) for a query PubChem cannot search

`pubchem_get_compound_details` tool

Up to 100 CIDs per call (the rest returned in unprocessed); 27 available properties, defaulting to a core set of 14
Optional descriptions (descriptionOffset/maxDescriptions, default 3, max 20) and classification (FDA, MeSH, ATC) cover the first 10 CIDs only, the rest listed in skippedCids. Optional synonyms (synonymOffset/maxSynonyms, default 20, max 100) and a Lipinski/Veber drug-likeness check cover every found CID
Per-CID found: false separates a nonexistent CID from a compound with no data

`pubchem_get_compound_image` tool

Single CID; size is "small" (100x100) or "large" (300x300, default)
Returns base64-encoded PNG plus width/height
Typed cid_not_found error when PubChem has no record for the CID

`pubchem_get_compound_3d_structure` tool

Single CID; format="json" (default) returns parsed atoms (element + x/y/z) and bonds, format="sdf" returns the raw V2000 SDF text
maxAtoms/maxBonds cap the JSON preview (default 200 each); atomCount/bondCount always report the full totals, with any capping disclosed via enrichment
includeRawSdf bypasses the default 500-line cap on the raw SDF text
Optional includeAlternateConformerIds lists conformer IDs beyond the default
Typed no_3d_structure error when PubChem has no computed 3D coordinates (large molecules, mixtures, some salts)

`pubchem_get_compound_xrefs` tool

Single CID; one or more xrefTypes: CAS, EC, RN, RegistryID, PatentID, PubMedID, GeneID, ProteinGI, TaxonomyID
CAS and EC are the numbers deposited for the compound, every distinct value ordered by how many source records deposited it, with those counts in sourceCounts. RN is PubChem's unranked registry-number list: the CAS number sits beside deprecated and related CAS RNs and EC numbers
ProteinGI currently returns no data from PubChem; use GeneID for gene/protein associations
maxPerType up to 500 (default 50), with one offset applied to every type; each type reports totalAvailable and truncated. PubMedID comes newest first
A type that fails to load is named in failedTypes and the others still return; the call fails only when a type fails and no type other than ProteinGI (which PubChem no longer serves) loads. An empty result says whether the compound has none of the requested types or the CID may be mistyped

`pubchem_get_compound_safety` tool

Up to 25 CIDs per call (the rest returned in unprocessed)
Returns the GHS signal word, pictograms, H-codes, and P-codes merged across sources, plus classifications[] with each source's own label; precautionary statements carry a decoded flag
Per-CID status: ok, not_classified (notifiers found no GHS hazard), no_ghs_data (no deposited classification), or cid_not_found, so a bad CID never reads as "no hazards on file"

`pubchem_get_bioactivity` tool

Single CID; filter by outcomeFilter (active/inactive/all, default all), targetGeneId/targetAccession, and assayType (any of confirmatory/screening/summary/other); an assay must pass every filter set
A target filter matches any identifier tied to the same target, so Gene ID 5742, UniProt P23219, and RefSeq NP_542158 all reach the same COX-1 assays
Each result carries the assay's assayType and the PubMed IDs it cites (pmids, newest first)
Up to 100 results per page (default 20); offset reaches the rest. A multi-target assay reports the matched target and lists the others under otherTargets
Reports totalAssays/activeCount/inactiveCount for the whole compound and filteredCount/returnedCount for the page; notices say whether there is no data, the filter excluded everything, or offset is past the end

`pubchem_get_compound_interactions` tool

Single CID; one or more kinds — drug-food (PUG View), target, drug-drug (DrugBank); default ["drug-food"], and an empty drug-food page points at target
target gives one entry per target the compound's assay summary names: a Gene ID with the accessions the table pairs with it, or an identifier it never pairs. A Gene ID and an accession that no row pairs are separate entries even when they name the same protein (erlotinib's ERBB2 appears as accession:P04626 and as GeneID:2064). Each entry names the target from a batched gene or protein summary lookup, plus the GeneID: or accession: value pubchem_get_bioactivity filters on, and states the assay counts by outcome and the most potent Active value with its AID. Active targets come first, most potent first. If a name lookup fails or does not answer within a few seconds, the entries keep their identifier and the notice says so
maxEntries per kind per page (max 50, default 10); offset counts records (targets, for target), up to 2,147,483,646. Each kind pages independently, reported in paging[] (totalRecords/nextOffset/truncated)
A kind that fails is named in failedKinds and the others still return. The notice offers a retry only for a failure a retry can clear (timeout, rate limit, network error, unreadable response, 5xx other than 501); an HTTP 400, 403, or 501, or a response in a shape the server does not expect, fails the same way on every call. drug-drug comes from PubChem's SDQ service, which refuses automated requests, so it lands in failedKinds and a retry will not help

只显示了开头部分；其余内容请在仓库中阅读

Pubchem MCP Server

概览

PopNx MCP 的三大支柱

它能帮你做什么

安装

安装之前

或者在你的电脑上运行

或者在你的电脑上运行

或者在你的电脑上运行

或者在你的电脑上运行

需要你填写的值

它能做什么

基础检查i

作者与仓库一致

仍在维护

有许可证

端点有响应

使用 OAuth 登录

工具描述中没有隐藏指令

与“搜索与 AI 记忆”中的其他服务器比较i

常见问题

替代选择

Context7

Codebase Memory

Exa

作者的 README

Overview

Tools

Resources

Skills

Capability reference

pubchem_search_compounds tool

pubchem_get_compound_details tool

pubchem_get_compound_image tool

pubchem_get_compound_3d_structure tool

pubchem_get_compound_xrefs tool

pubchem_get_compound_safety tool

pubchem_get_bioactivity tool

pubchem_get_compound_interactions tool

`pubchem_search_compounds` tool

`pubchem_get_compound_details` tool

`pubchem_get_compound_image` tool

`pubchem_get_compound_3d_structure` tool

`pubchem_get_compound_xrefs` tool

`pubchem_get_compound_safety` tool

`pubchem_get_bioactivity` tool

`pubchem_get_compound_interactions` tool