"Retrieving Markdown Files from a Database" matching MCP servers:

MCP server for the STRING protein–protein interaction database, hosted by STRING at mcp.string-db.org. Adapted for LLM grounding: responses are size-limited and include metadata and notes on interpretation and next steps. Tools cover identifier resolution, interaction networks and evidence, functional and PPI enrichment, and sequence similarity search.

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).

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

Provides direct SQL access to a locally hosted Reactome database, enabling schema discovery, guarded read-only queries, and ergonomic helpers over the full relational schema.

An MCP server that provides tools for searching and fetching protein data from the UniProt database using the unipressed library.

Enables complex searches, sequence mapping, genomic analysis, and metadata retrieval for non-coding RNA sequences from the RNAcentral database.

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.

Enables AI assistants to search and retrieve bacterial strain details, taxonomy, culture media, 16S rRNA sequences, and genome information from the BacDive database through MCP tools.

Enables LLM-powered applications to look up bacterial and archaeal taxonomy, search genomes, browse and navigate the taxonomic tree, and compare genomes or find phylogenetic paths between taxa. It works out of the box with a built-in reference dataset covering major phyla and can be pointed at full Genome Taxonomy Database TSV files for comprehensive queries.

Retrieve genomic data from EGA, ENA, ENCODE, GEO and NCBI, read bounded regions from indexed BAM/CRAM, VCF and bigWig files, and query source-attributed reference evidence. Runs locally with 23 MCP tools. MIT-licensed; research use.

Provides access to the STRING protein-protein interaction database for mapping identifiers, retrieving interaction networks, and performing functional enrichment analysis. It enables users to explore protein partners, pathways, and cross-species homology through natural language interactions.

Provides standardized access to aging and longevity research data from the OpenGenes database, enabling AI assistants to query comprehensive biomedical datasets through SQL and structured interfaces.

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 searching, retrieving, and downloading protein structure data from the RCSB Protein Data Bank. Supports intelligent protein structure search, comprehensive data retrieval, and multiple file format downloads for bioinformatics research.

Provides seamless access to UniProtKB protein database, enabling queries for protein entries, sequences, Gene Ontology annotations, full-text search, and ID mapping across 200+ database types.

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.

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.

Enables AI assistants to query genetic variant data, gene constraints, and population genetics information from the gnomAD (Genome Aggregation Database) through its GraphQL API. Supports searching for genes and variants, retrieving constraint scores, analyzing population frequencies, and accessing genomic coverage data.

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

Enables AI agents to search, filter, download files, and generate reports from the IGVF Data Portal using natural language commands.

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.

Enables querying the gnomAD genome aggregation database for variant, gene, and region information.

Enables AI agents to search and retrieve compounds, drugs, diseases, pathways, genes, enzymes, glycans, modules, and KO entries; fetch full parsed flat-file entries by ID; and list database contents through keyless REST tools.

Enables querying and browsing ontologies from the EBI Ontology Lookup Service, including searching for terms, retrieving term details, and navigating ontology hierarchies via natural language.

Enables searching and retrieving cancer-genomics projects, cases, and genomic data files — including TCGA, TARGET, and CPTAC — via keyless, open-access metadata tools. Supports filtering by primary site, project, or data category, and can route plain-English questions to the right tool automatically.

Enables searching cancer genes and curated variants from CIViC, retrieving associated diseases, therapies, and graded evidence items and assertions for clinical interpretation.

Enables AI agents to query the PomBase fission yeast model-organism database for genetic and molecular data through the Pipeworx MCP gateway.

Enables querying and retrieving bacterial and viral genomic data, features, antimicrobial resistance, and epitopes from the BV-BRC API using natural language.

Enables discovery of CPIC gene–drug pairs and guidelines, translation of source-supported diplotypes and allele evidence, and browsing or matching of prescribing recommendations via read-only tools. Data comes from the public CPIC Database API with clinical context from ClinPGx.