Chembl MCP Server vs Noodle Biomedical Lit… | AllMCPs
Side-by-Side Model Context Protocol Comparison
Chembl MCP Server vs Noodle Biomedical Literature Discovery MCP
In-depth architectural comparison of the Chembl MCP Server and Noodle Biomedical Literature Discovery MCP MCP servers. Compare execution transports, security boundaries, tool capabilities, quality scores, and ready-to-paste client installation snippets for Claude, Cursor, Windsurf, and VS Code.
At a Glance & Executive Verdict
Chembl MCP Server
Biology & Bioinformatics · Local stdio
Quality: 52/100 (Good) | Auth: No auth required
Noodle Biomedical Literature Discovery MCP
Biology & Bioinformatics · Remote HTTP/SSE
Quality: 76/100 (Great) | Auth: No auth required
Verdict Summary: Choose Chembl MCP Server if you need specialized Biology & Bioinformatics tools running via a local process. Choose Noodle Biomedical Literature Discovery MCP if your workspace requires Biology & Bioinformatics integration with remote web transport. Both servers can be configured concurrently in your client's mcpServers manifest.
Which MCP Server Should You Choose?
Choose Chembl MCP Server when:
You need dedicated capabilities in the Biology & Bioinformatics domain.
You prefer local stdio subprocess transport architecture.
Your security boundary fits: No auth required (Free / Open Source).
Link compounds to protein targets, rank bioactivity, and look up drug mechanisms and indications.
Official public, read-only Model Context Protocol server from Helena Bioinformatics for biomedical literature discovery. Agents can search PubMed and scholarly research, resolve PMID, DOI, and PMCID identifiers, inspect publication metadata, find related papers, traverse bounded citation graphs, explore semantic literature neighborhoods, and check corpus coverage. Use the hosted Streamable HTTP endpoint https://api.helena.bio/noodle/v1/mcp; no npm or npx package is required.
Find compounds by name / ChEMBL ID / InChIKey, or run a structure search (exact \
chembl_get_bioactivities
The flagship compound↔target bridge: bioactivity measurements for a molecule, a target, or **both** (the compound×target pair), ranked on `pchembl_value`, or the measurements without one via `potency_view`. Large sets spill to a canvas.
chembl_search_targets
Resolve a protein / gene symbol / UniProt accession to the ChEMBL target ID `chembl_get_bioactivities` needs.
chembl_get_drug_info
Drug pharmacology — mechanism(s) of action, molecular target(s), action type, first-approval year, and clinical indications.
chembl_get_assay
Assay provenance behind a bioactivity row — type, target, organism, and ChEMBL's 1–9 confidence score.
chembl_dataframe_query
Run a read-only SQL `SELECT` over the bioactivity rows spilled to a canvas — rank, group, dedupe, aggregate across the full set.
chembl_dataframe_describe
List the tables and columns staged on a canvas, so you can write correct SQL before querying.
chembl_dataframe_drop
Drop a named staged table from a canvas. Opt-in via `CHEMBL_DATAFRAME_DROP_ENABLED=true` — absent from `tools/list` when off, since TTL already reclaims staged tables.
Noodle Biomedical Literature Discovery MCP Tools (6)
Natural-language biomedical literature search
PMID, DOI, and PMCID resolution
Publication and work metadata lookup
Bounded citation and semantic graph traversal
Corpus size, source, freshness, and coverage metadata
Hosted Streamable HTTP access
Ready-to-Paste Client Configurations
Paste either (or both) of these JSON server blocks into your client config file (e.g. claude_desktop_config.json or ~/.cursor/mcp.json).
Chembl MCP Server is categorized under Biology & Bioinformatics and uses a local stdio subprocess. In contrast, Noodle Biomedical Literature Discovery MCP belongs to Biology & Bioinformatics using remote streaming HTTP/SSE transport. Select Chembl MCP Server when you need capabilities focused on biology & bioinformatics and Noodle Biomedical Literature Discovery MCP when you require tools for biology & bioinformatics.