"Services or tools available for free without requiring an API key" matching MCP servers:

Enables AI agents to query Human Phenotype Ontology clinical phenotype terms, navigate term hierarchies, and retrieve gene-disease and disease-phenotype annotations through keyless MCP tools.

Provides a collection of MCP servers for computational chemistry tasks including molecular generation and retrosynthesis. Also offers property prediction and molecule pricing capabilities.

Enables MCP-capable AI clients to characterize proteins end to end: PDB/mmCIF validation, sequence extraction and typing, pLDDT confidence summaries, metal-site geometry with bidentate chelate detection, GROMACS trajectory metrics and plots, and live UniProt, AlphaFold DB, and RCSB lookups. Also ships a point-and-click Protein Lab web UI (and a persistent run registry) so students and wet-lab biologists can get the same results without any client setup.

Enables deep probabilistic analysis of single-cell omics data using scvi-tools through natural language. Supports SCVI for scRNA-seq analysis, SCANVI for cell type annotation, TOTALVI for multi-modal RNA/protein data, and PEAKVI for scATAC-seq analysis.

A specialized MCP server for Metal-Organic Framework research that provides tools for database searching, structural optimization, and energy calculations via ASE. It enables scientific workflows by allowing users to interact with MOF data and perform chemical simulations through a standard SSE interface.

Enables searching cryo-EM density maps in EMDB and raw datasets in EMPIAR, with filtering by resolution, keyword, and cross-referencing between the two databases.

Enables discovery and querying of public OpenBind structure-affinity datasets, experimental binding events, benchmark results, and live Fragalysis targets and observations through read-only REST endpoints without requiring an API key.

This server enables multi-agent conversations for interacting with Cirro's biological data platform through its OpenAPI interface, auto-generated using AG2's MCP builder.

Enables language models to search biomedical literature, fetch sequences, and follow links across Entrez databases through eleven read-only tools wrapping the nine NCBI Entrez E-utilities. It handles URL building, pacing, redirects, response caps, and API-key redaction so queries can be answered without a browser or scraping.

Enables MCP clients to annotate and classify single human genetic variants in any notation, returning an auditable points-based ACMG verdict with its criteria, gnomAD frequencies, in-silico predictors, ClinVar data, and per-transcript consequences. It is read-only, requires no account or API key, and keeps answers compact while linking back to the source.

An MCP server that gives Claude access to NCBI Datasets v2 — search genome assembly metadata, retrieve taxonomy records, and download data packages without leaving your conversation.

Provides a Model Context Protocol server for accessing and querying biomedical data from BioThings services, including gene, variant, chemical, and taxon annotations.

Enables users to search rRNA sequences by organism, accession, or taxonomy, retrieve detailed sequence metadata, evaluate probes and primer pairs, and list available databases and taxonomies through MCP tools.

An MCP server for querying the KEGG bioinformatics database, providing tools, resource templates, and guided prompts for pathways, genes, compounds, and more.

Parses MS-DIAL binary lipidomics outputs and runs standard analyses server-side, returning compact summaries so an LLM can drive full lipidomics analysis without exposing raw matrices.

An MCP server that enables single-cell RNA sequencing analysis through natural language, supporting data processing, visualization, and analysis tasks without requiring coding knowledge.

Enables searching ENA's public sequencing data by organism, study, platform, country or date, retrieving FASTQ/BAM download URLs and checksums, and discovering available result types and fields.

An MCP server that exposes the KEGG REST API — pathways, genes, compounds, reactions, enzymes, diseases, drugs, modules, orthology, glycans, and BRITE hierarchies, with cross-database linking. Provides 34 tools and 8 resource templates.

Enables AI agents to search EBI BioSamples metadata for biological samples such as cell lines, tissues, and organisms by free-text keyword, and to fetch individual records by accession to retrieve taxId, organism, and characteristics like tissue, sex, and cell type. It can run as a hosted gateway endpoint or locally over stdio via npx.

MCP-native scientific skills for reproducible computational biology and AI-driven drug-discovery workflows. It combines deterministic scientific tools with an MCP server to give AI agents real computational capabilities.

An MCP server for running local LLMs using llama-cpp-python, with built-in tools for generating drug-like molecule SMILES.

Enables AI agents to resolve genes, diseases, chemicals, variants and species to normalized ids, search ~36M PubMed abstracts and PMC full texts by free text or entity, and retrieve the machine-extracted relations between them with the supporting sentences and PMIDs. Supports auditing individual relations with full evidence passages and pulling per-article entity annotations with character offsets.

Enables querying NCI Thesaurus and other cancer-research vocabularies served by NCI Enterprise Vocabulary Services, providing codes, synonyms, definitions, and hierarchical relationships via MCP tools.

Enables AI assistants to create, monitor, and manage computational tasks through GA4GH Task Execution Service (TES) functionality. Provides seamless access to TES-compliant services for executing bioinformatics and scientific computing workflows.

Federates 13 gene-related MCP backends (gnomAD, GTEx, etc.) behind a single Streamable HTTP endpoint with collision-free namespacing and search-based tool discovery.

An MCP server that wraps R scripts for microbiome and amplicon (16S/ITS) analysis, providing tools for alpha/beta diversity, differential abundance, networks, and more, with PNG/PDF outputs.

Enables users to look up yeast genes/loci, search genes and alleles by free text, and retrieve Gene Ontology annotations from the Saccharomyces Genome Database.

Enables AI agents to browse the Gene Ontology through the EBI QuickGO API, including keyword search for GO terms, retrieval of a term's name, aspect, definition and synonyms by id, and listing the GO annotations tied to a UniProt accession. Runs keyless over HTTP or as a local stdio server, with an optional gateway route that lets plain-English questions be answered without choosing tools manually.

Folklore MCP 1.7.0 provides ACMG/AMP germline variant classification, gene profiles, ClinGen disease associations and scientific literature. Eleven tools. Free Streamable HTTP; no account or API key required.

Resolves free-text condition and disease strings — trial-registry condition fields, drug-label indications, hand-typed wording — onto the Mondo Disease Ontology, returning the best term id and label along with a trustworthy match-quality label (exact label/synonym, broader, narrower, fuzzy, or no-match) plus cross-ontology xrefs. Optionally expands a resolved term to all of its descendant ids for building subtype-inclusive registry filters.