Best Alternatives to Pubchem MCP Server

Chembl MCP Server

Runtime: bunx

Link compounds to protein targets, rank bioactivity, and look up drug mechanisms and indications.

Pubmed MCP Server

Runtime: bunx

Comprehensive PubMed MCP Server to search, retrieve, and analyze biomedical literature from NCBI.

Medplum MCP

Runtime: Remote (SSE)

Securely access and manage FHIR healthcare data stored in Medplum.

Healthcare Fhir MCP

Runtime: npx

Healthcare Fhir tools for AI agents. Capabilities: search patients, get patient, search cond...

Spiderbrain

Runtime: npx

Deterministic context layer for your codebase: change impact, blast radius, answers with receipts.

Galaxy MCP

Runtime: uvx

MCP server for Galaxy bioinformatics platform - connect, execute tools, and manage workflows

Clinical Trials AI MCP

Runtime: npx

MCP server for clinical trials ai. Features search trials, check eligibility, get trial deta...

Ncbi Eutils

Runtime: Remote (SSE)

NCBI E-utilities — federated Entrez search/fetch (PubMed/Gene/Nucleotide/…)

Prism

Runtime: npx

Local-first repo intelligence for agents: DNA, health, blast radius, and Dispatch jobs.

Uniprot MCP Server

Runtime: bunx

Protein research over UniProtKB — search by function, fetch curated records, map IDs, proteomes.

Rosetta MCP Server

Runtime: uvx

Rosetta/PyRosetta protein modeling and Biotite translation for computational biology

EasyDocForms

Runtime: npx

Healthcare intake for agents: import blank PDFs, create patient fill links, fetch completed PDFs.