"RAG (Retrieval-Augmented Generation) system that can store papers and web pages" 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 GPU-accelerated scientific computing capabilities including symbolic mathematics, quantum wave mechanics simulations, molecular dynamics, and neural network training through four specialized MCP servers.

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

MCP server that exposes the UniProt REST API to LLM clients, enabling search and retrieval of protein data via tools like search_uniprotkb, get_entry, and map_ids.

Enables LLM agents to search biomedical literature, retrieve article details, find related papers, manage caching, and download open-access full texts through MCP with structured, agent-friendly responses.

Enables AI coding agents to search academic papers, resolve biomedical entities, mine relations, and traverse citation graphs using Semantic Scholar and PubTator3, with local caching for reproducibility.

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.

A Model Context Protocol server that enables retrieval of -omics data from sources like PDB, ChEMBL, UniProt, PubChem, and HUGO.

Access to 1000 Genomes Project dataset, hosted online in Dnaerys variant store

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.

Annotate variants by with a deep and rich set of data. Can annotate: genetic change, rsID, CAid, HGVS (g./c./p.), protein change.