"A Python server using FastAPI to expose public web API endpoints to an agent" matching MCP servers:

An MCP server providing public plant bioinformatics APIs including UniProt, NCBI, InterProScan, PDB, AlphaFold, Ensembl Plants, and web-based resources like Sol Genomics and BAR, without local data. It supports gene lookups, protein summaries, structure retrieval, and functional annotations through natural language.

Enables compiling typed decision queries into the smallest decision-sufficient evidence context with machine-checkable Context Certificates, providing auditable executable-biology inference through local MCP tools.

Enables AI agents to read and manipulate networks, tables, visual styles, and more in a live Cytoscape Web session through natural language, by connecting over Chrome DevTools Protocol.

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.

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

Enables prediction of blood-brain barrier permeability for drug molecules via machine learning, with molecule name lookup, plain-language explanations, similar drug search, and applicability domain checks. Exposes these as MCP tools and orchestrates them via a LangGraph agent.

Enables genomic sequence analysis through the Evo 2 model, supporting DNA sequence scoring, embedding, generation, and variant effect prediction with multiple model checkpoints (7B, 40B, 1B parameters).

Empowers AI agents with direct access to the official ClinicalTrials.gov database, enabling programmatic searching, retrieval, and analysis of clinical study data through a Model Context Protocol interface.

An MCP server that enables AI coding assistants to interact with Rosetta, PyRosetta, and Biotite for running RosettaScripts, validating XML, translating between Rosetta and Biotite, scoring structures, and querying documentation.

Enables gene set enrichment analysis using the Enrichr API across hundreds of gene set libraries including Gene Ontology, pathways, diseases, tissues, drugs, and transcription factors. Returns only statistically significant results for interpretation.

Enables variant annotation and effect prediction using the Ensembl VEP API, with support for batch and single queries.

A Model Context Protocol (MCP) server that provides access to the Protein Data Bank (PDB) - the worldwide repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies.

A production-ready Model Context Protocol (MCP) server that provides comprehensive access to the BioOntology API for searching, annotating, and exploring over 1,200 biological ontologies.

A comprehensive Model Context Protocol (MCP) server that provides access to the AlphaFold Protein Structure Database through a rich set of tools and resources for protein structure prediction analysis.

A comprehensive Model Context Protocol (MCP) server providing advanced access to the ChEMBL chemical database.

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

🔍 Enable AI assistants to search, access, and analyze PubMed articles through a simple MCP interface.

🔍 A biomedical literature annotation and relationship mining server based on PubTator3, providing convenient access through the MCP interface.

A Model Context Protocol server providing programmatic access to 3D protein structural data from RCSB PDB, PDBe, and UniProt, enabling search, retrieval, comparison, and analysis of protein structures.

A collaborative BrAPI v2.1 workspace for multi-agent research via MCP, enabling search and retrieval of studies, germplasm, genotypes, and more across any BrAPI v2-compliant server.