"MCP Service for Debugging Local Databases" matching MCP servers:

Enables AI clients to connect to Galaxy instances, inspect histories and reports, discover tools and workflows, submit analyses, and monitor their results via interactive cards.

Provides protein family, domain, and functional annotation using InterProScan, supporting local or API backends.

This server enables multi-agent conversations for interacting with Cirro's biological data platform through its OpenAPI interface, auto-generated using AG2's MCP builder.

A Model Context Protocol server that interfaces with Biomart databases, allowing models to discover biological datasets, explore attributes/filters, retrieve biological data, and translate between different biological identifiers.

Provides LLMs with structured access to critical biomedical databases including PubTator3 (PubMed/PMC), ClinicalTrials.gov, and MyVariant.info through the Model Context Protocol.

Enables protein structure and sequence searches using FoldSeek, with support for multiple databases, automatic model downloads, and structured job management.

Provides AI-powered access to major biological databases for GWAS and bioinformatics research. Enables natural language queries for protein, gene, variant, pathway, and drug discovery analysis.

Enables building and analyzing signalling networks from interaction databases through a Model Context Protocol server.

Enables querying HIV-1 antibody neutralization potency data (IC50/IC80/ID50) and HIV T-cell epitope and antibody-binding-site records from LANL databases.

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

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.

Connects to NCBI E-utilities for searching, fetching, and linking biological data across Entrez databases.

Enables AI assistants to create, monitor, and manage computational tasks through GA4GH Task Execution Service (TES) functionality. Provides seamless access to TES-compliant services for executing bioinformatics and scientific computing workflows.

Enables functional enrichment analysis of gene lists against multiple pathway and ontology databases, plus gene/protein identifier conversion and cross-species ortholog mapping.

Enables AI agents to query clinical genomics databases, retrieve supporting literature, analyze population genetics, and visualize biological pathways.

Unified MCP server providing AI-agent-ready access to AlphaFold, PubMed, ChEMBL, Ensembl, and 37+ scientific databases.

Executes SPARQL queries against biological and biomedical RDF databases from the RDF Portal, with additional REST API integrations for bioinformatics resources.

A server providing access to NCBI E-utilities API for searching and retrieving data from databases like PubMed, Protein, and Nucleotide.

Search UniProtKB by protein function, fetch curated records, map IDs across databases, and pull reference proteomes, taxonomy, and sequences via MCP. Supports both STDIO and Streamable HTTP transports.

Wraps NCBI BLAST+ blastp into a FastMCP service for auditable protein homology searches with local output artifacts and structured metadata.

An MCP server for MARRVEL that enables AI agents to access genetics databases and variant analysis tools for rare disease research.

An advanced integrated MCP server platform that combines 600+ tools and multiple biomedical databases to enable comprehensive information retrieval across molecules, proteins, genes, and diseases for accelerating therapeutic research.

An MCP server that grounds protein research in the UniProt SPARQL endpoint, providing tools for querying proteins, sequences, variants, diseases, and more via intent-named tools and raw SPARQL.

Enables language models to search biomedical literature, fetch sequences, and follow links across Entrez databases through eleven read-only tools wrapping the nine NCBI Entrez E-utilities. It handles URL building, pacing, redirects, response caps, and API-key redaction so queries can be answered without a browser or scraping.

Enables AI assistants to clean PDB structures and run initial-stage energy relaxation for biomolecular modeling. It provides a structured workflow for preparing structures before production molecular dynamics or coarse-graining pipelines.

MCP server that provides tools to query harmonized gene-disease validity data from the Gene Curation Coalition, supporting consensus and conflict detection for gene-disease assertions.

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.

Enables AI agents to retrieve cited pharmacogenomic and gene-variant information, including drug–gene guidance from CPIC/DPWG and rsID lookups, so responses can quote curated sources instead of relying on memory. A local package also lets users read raw DNA files on their own computer without sending the file data to the remote service.

A Model Context Protocol (MCP) server for interacting with Gen3 data commons, with GraphQL query validation to reduce hallucinations.

An MCP server for searching and accessing RNA sequencing datasets from the European Nucleotide Archive (ENA), supporting bulk, single-cell, and spatial transcriptomics with advanced filtering and download capabilities.