"Servers Offering MCP Prompts as Prompt Primitives" matching MCP servers:

Exposes phylogenetic tree validation, analysis, styling, export, and Java-based rendering as 21 MCP tools, 3 resources, and 2 prompts for AI assistants. Delegates parsing and rendering to the FigTreeKit kernel, returning reproducible CLI commands and structured artifacts.

Exposes a bio-hybrid neuromorphic simulation pipeline (SNN, consciousness proxies, FinalSpark NeuroPlatform) as MCP tools, resources, and prompts for AI assistants like Claude, Cursor, and VS Code.

MCP server exposing REINVENT4 generative molecular-design operations as validated, LLM-callable tools for drug discovery, including sampling, transfer learning, reinforcement learning, and molecular analysis.

Provides read-only access to the ProPaths verified protein interactome, letting AI agents search proteins, retrieve mechanistic interaction details, and explore pathway ontology through MCP tools, resources, and prompts.

Enables AI assistants to rapidly gather and synthesize structural, chemical, conservation, and literature data about protein binding pockets for drug-target triage. Useful as a reconnaissance step before computational binder design.

MCP server offering verified bioinformatics tools for sequence utilities and statistics, backed by BioPython/scipy. Enables AI agents to perform accurate GC content, translation, ORF finding, motif scanning, and statistical tests through natural language.

Enables LLM agents to search EMDB cryo-EM maps, look up UniProt proteins, compute ESM-2 sequence embeddings, retrieve cryo-EM maps from a protein sequence via a two-tower model, and search GEO DNA-methylation arrays, all through typed tools with structured output. Ships with a 40-question evaluation harness that runs Claude as the MCP client.

An MCP server that gives AI assistants access to biological and biomedical RDF databases via SPARQL at the RDF Portal, as well as selected REST APIs (NCBI E-utilities, UniProt, ChEMBL, PDB, Reactome, Rhea, MeSH, and more).

Enables AI agents to resolve and cross-reference biological entities such as genes, proteins, and aliases across authoritative databases like HGNC, NCBI Entrez, and UniProt, with confidence scores and source citations.

Enables AI assistants to query the eggNOG 7 database in natural language for protein lookups, orthologous groups, pairwise orthologs, protein families, taxonomy, and database statistics. Also delivers structured functional annotations such as KEGG KO and GO terms with confidence scores, plus an index of bulk-downloadable data files.

This server provides agents with access to key data across UniProt, RCSB PDB, and ChEMBL archives. It enables the completion of complex biochemical and drug discovery tasks by offering structured tool endpoints.

Reads raw lab-instrument files (microscopy, mass spectrometry, chromatography, flow cytometry, NMR, electrophysiology, spectroscopy, plate readers, qPCR) without vendor software, returning metadata, images, spectra and traces as JSON. It also checks files for damage, runs common analyses, and exports to open formats such as OME-TIFF, OME-Zarr, mzML, Parquet and NWB.

Enables AI-powered genomic variant analysis including variant impact prediction, regulatory element discovery, and batch variant scoring. Currently operates in mock mode as a proof-of-concept awaiting the public release of Google DeepMind's AlphaGenome API.

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

MCP server for biopharma software infrastructure offering FDA 21 CFR Part 11 audit trails, CDISC SDTM/Allotrope data exports, 4PL dose-response curve fitting, and HIPAA PII/PHI redaction through 10 Zod-validated tools.

MCP server that exposes DECIMER image-to-SMILES functionality as tool calls.

Exposes the NGS360 bioinformatics platform REST API as MCP tools, enabling AI assistants to manage sequencing runs, projects, workflows, and more through natural language.

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.

Exposes the Adaptyv Foundry protein characterization API as MCP tools, enabling AI assistants to interact with experiments, targets, sequences, and results in natural language.

Exposes pipen bioinformatics pipelines as MCP tools, allowing AI assistants to discover and run complex workflows through a progressive disclosure interface.

Enables AI assistants to automate iTOL phylogenetic tree visualization workflows, including tree inspection, taxonomy and monophyly analysis, annotation template generation, batch uploads, and export through 33 tools, 3 resources, and 2 prompts.

Provides a natural language interface for scRNA-Seq analysis using the Scanpy library, supporting operations such as data preprocessing, clustering, and visualization. It enables AI agents and clients to perform complex single-cell transcriptomics workflows through the Model Context Protocol.

Enables AI agents to resolve marine species names to OBIS taxon records, retrieve georeferenced ocean occurrence records with optional date filtering, and pull aggregate statistics such as record counts, contributing datasets, and observed year ranges. Queries the Ocean Biodiversity Information System keylessly over the Pipeworx gateway or as a local stdio server.

An MCP server that provides access to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, offering 30 tools for searching and analyzing biological data like pathways, genes, and compounds. It supports integration with LangChain and Ollama to enable LLMs to interact with comprehensive genomic and chemical datasets.

Enables looking up drug and molecule data — identifiers such as InChIKey, SMILES, CAS, and ChEMBL IDs, plus measured and computed properties and drug information — across PubChem, ChEMBL, and Wikidata. Every returned value carries its cited source, and it covers small molecules, peptides (including modified and cyclic forms), and conjugates such as antibody–drug conjugates.

Enables users to search and retrieve 3D cryo-EM and electron-tomography density maps by keyword or entry ID, returning details such as resolution, structure-determination method, sample, and release date.

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.

Provides MCP tool adapters for Bioconductor methods like limma, DESeq2, and fgsea, enabling statistical analysis of omics data through containerized R execution. It serves as a bridge between MCP clients and bioinformatics tools for reproducible research workflows.

Enables AI agents to query Protein Data Bank in Europe (EBI) structural data by 4-character PDB ID, retrieving entry summaries, molecule/entity listings with chain lengths, and SIFTS cross-database mappings to UniProt accessions and residue ranges. Runs as a hosted gateway endpoint or a local stdio server with no authentication required.

Enables searching EBI BioStudies, a keyless database of biological study descriptions, by keyword and retrieving full metadata for a single study by accession, including title, abstract, release date, and link counts. Results tie studies across EBI archives such as ArrayExpress and PRIDE, so agents can locate and inspect study records without authentication.