pubchem-mcp-server
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- FlicenseNot gradedqualityDmaintenanceEnables AI assistants to search and retrieve chemical compound information, structures, and physical properties from the PubChem database. It supports querying via compound names, SMILES notation, or CIDs to provide detailed molecular data for chemical analysis.5-
- AlicenseBqualityDmaintenanceEnables comprehensive access to PubChem's chemical database with over 110 million compounds. Supports chemical searches, structure analysis, bioactivity data, safety information, and molecular property calculations through 30 specialized tools.30MIT
- AlicenseNot gradedqualityBmaintenanceProvides access to the NIH PubChem chemistry compound database, enabling queries for compound synonyms and other data through natural language.11 npmMIT
- FlicenseBqualityFmaintenanceExtracts basic chemical information and drug data from the PubChem API. It enables users to retrieve molecular details such as SMILES, IUPAC names, molecular formulas, and synonyms for specific compounds.311-
- AlicenseBqualityDmaintenanceEnables AI agents to search the Chemspace API for synthesizable building blocks and screening compounds using exact matches, substructure searches, and similarity searches by SMILES strings.31MIT
- AlicenseBqualityDmaintenanceEnables users to retrieve chemical safety information including compound properties, GHS safety classifications, and toxicity data from PubChem database using compound names or CIDs. Supports batch queries with caching for efficient chemical safety research and analysis.3MIT
TDQS
Scored across 10 tools
Several tools overlap in purpose: 'pubchem_get_bioactivity' and 'pubchem_get_compound_interactions' both return activity/target data, with interactions including bioactivity-like entries. Also, 'pubchem_get_summary' and 'pubchem_get_compound_details' both provide descriptive info for compounds, though summary supports other entities. The distinction between bioactivity and interactions is particularly blurry for agents.
All tools follow a consistent pattern: 'pubchem_' prefix followed by a verb ('get', 'search') and a target object ('compound', 'assays', 'summary'), with specific qualifiers. For example, 'pubchem_get_compound_details', 'pubchem_get_compound_image', 'pubchem_get_bioactivity'. No mixed naming conventions or irregular verbs.
With 10 tools, the count is within the ideal range (3-15) and each tool serves a distinct data retrieval purpose. However, some tools like 'pubchem_get_compound_3d_structure' and 'pubchem_get_compound_image' are narrow utilities, but they still cover necessary compound data. No obvious bloat or excessive specialization.
The tool set is heavily focused on reading/querying compound data, covering search, details, images, structures, safety, bioactivity, interactions, and summaries. Missing operations include any update/delete (not applicable for a database), but more importantly, there's no tool for getting compound synonyms directly (only via details with synonyms flag), and no tool for retrieving patents or other xrefs beyond what's in xrefs. The lack of a direct 'get_compound_by_name' is a gap; search requires a separate step. Also, no support for handling mixtures or salts explicitly. Overall, core lookup is covered but some ancillary data types are missing.