"Access to filesystem resources" matching MCP servers:

Provides read-only access to the ProPaths verified protein interactome, letting AI agents search proteins, retrieve mechanistic interaction details, and explore pathway ontology through MCP tools, resources, and prompts.

Enables interaction with MGnify metagenomics resources and tools through the Model Context Protocol. Provides access to MGnify's API for querying and analyzing metagenomic datasets and related biological information.

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.

An MCP server that provides standardized access to biomedical knowledge bases and resources, enabling AI systems to retrieve verified information from sources like bioRxiv, EuropePMC, and various protein/gene databases.

MCP server for querying gene annotations, full-text gene search, and species taxonomy via MyGene.info. Enables AI agents to access gene data through natural language questions.

This server provides access to InterPro protein family, domain, and functional-site classification data from EBI. It allows querying protein annotations through natural language or direct tool calls.

Enables search and access to MGnify public microbiome studies, biome vocabulary, and ~57,000 MAGs and isolate genomes with completeness, contamination, and GTDB taxonomy.

Provides access to UniProt protein sequence and function knowledge base, enabling search and retrieval of protein entries, proteomes, taxonomy, and feature annotations.

Enables querying the BOLD Systems global DNA barcode database for specimen records, taxonomy, barcode sequences, and BIN clusters, with keyless access and FASTA-ready output.

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

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

Enables querying the EBI Expression Atlas for gene expression data across species and conditions. Part of the Pipeworx gateway, it provides access to baseline and differential expression studies.

A unified MCP server for biomedical research that connects AI systems to resources like Ensembl, EuropePMC, STRING, and more, enabling retrieval of verified domain-specific information.

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

Reproduces the in-silico toxicological profile of Heracleum sosnowskyi metabolites from Rassabina & Fedorov (2025) using open-source models for LD50 prediction, toxicity classification, chemical space clustering, and synthesis cost estimation.

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.

Grounds gene-nomenclature work in the HUGO Gene Nomenclature Committee (HGNC) dataset, enabling resolution of gene symbols and IDs to canonical HGNC identifiers, plus cross-references and batch operations.

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.

Enables coding agents to interact with the Reactome pathway database, including search, lookup, hierarchy traversal, SBML/SBGN export, and gene-set enrichment analysis.