"Chat with RAG (Retrieval-Augmented Generation)" matching MCP servers:

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

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.

Enables AI assistants to query and analyze genomics data from the GTEx Portal through 25 specialized tools for gene expression analysis, eQTL/sQTL associations, and genetic variant lookups across 54 human tissue types.

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

A comprehensive Model Context Protocol server providing access to over 110 million chemical compounds with extensive molecular properties, bioassay data, and chemical informatics tools from the PubChem database.

Provides access to BioThings.io APIs for comprehensive gene and variant annotations, enabling seamless integration of biological data into workflows.

Enables natural language querying and analysis of KEGG biological databases, including pathways, genes, compounds, reactions, diseases, and drugs.

A comprehensive Model Context Protocol (MCP) server for accessing the STRING protein interaction database. This server provides powerful tools for protein network analysis, functional enrichment, and comparative genomics through the STRING API.

Provides comprehensive access to the NCBI Datasets API, enabling genomic, taxonomic, and biological data operations through 31 specialized tools.

Enables molecular generation, optimization, and analysis through NVIDIA MolMIM API. Supports generating drug-like molecules with desired properties, extracting molecular embeddings, and exploring chemical space around seed molecules.

Unified genomic track, peak, and sequence retrieval tool for ENCODE, ChIP-Atlas, ReMap, GEO, and SRA/ENA with unified metadata, resolved DOI/PMID provenance, and direct FASTQ download without SRA toolkit.

Enables querying Ensembl genomic data including gene lookup, sequence retrieval, homology, variation, and variant effect prediction via MCP tools.

Provides access to AlphaFold predicted protein 3D structures from EBI, enabling retrieval of prediction metadata, summaries, annotations, and UniProt data.

MCP server for Ketcher chemical structure editor integration, enabling SMILES/MOL/InChI conversion, image generation, molecular property calculation, and validation.

Provides access to EBI's MetaboLights metabolomics study repository via an MCP gateway, enabling querying and retrieval of metabolomics data.

Provides access to the AlphaFold Protein Structure Database with tools for structure retrieval, confidence analysis, batch processing, and visualization.

Enables in-chat scientific viewers for molecular structures, sequence alignments, and slide images, plus data tools for searching structures, fetching sequences, aligning them, and drafting NGS analysis plans.

Enables search and retrieval of academic papers from PubMed database with advanced features like MeSH term lookup, publication statistics, and PICO-based evidence search.