"How to work with local files" matching MCP connectors:

Link compounds to protein targets, rank bioactivity, and look up drug mechanisms and indications.

Official answers about Helena Bioinformatics and its products, with citations to public sources.

BioBTreeA

bio.sugi

A unified biomedical graph database that integrates 50+ primary data sources — genes, proteins, compounds, diseases, pathways, and clinical data — into a single queryable graph with billions of cross-reference edges. Its native MCP server gives LLMs direct access to structured, authoritative biomedical data, complementing their reasoning with reliable identifiers and up-to-date database content.

EBI PRIDE Archive MCP — proteomics (mass-spectrometry) data repository.

MyVariant.info MCP.

RCSB PDB MCP — experimentally determined macromolecular structures.

Monarch biomedical knowledge graph — diseases, phenotypes, genes, variants

GWAS Catalog (EBI/NHGRI) MCP — curated catalog of genome-wide association studies.

EBI Expression Atlas MCP.

Human Protein Atlas (HPA) MCP — keyless.

PomBase MCP — the fission yeast (Schizosaccharomyces pombe) model-organism database.

UniProt MCP — protein sequence + function database.

InterPro MCP (EBI) — protein family / domain / functional-site classification.

Ensembl REST — vertebrate genomes, sequences, comparative genomics, variation

Bioregistry — meta-registry of biomedical identifier prefixes

Broad Institute gnomAD genomic variant database (GraphQL)

ChEMBL MCP — drug discovery database (EBI).

AlphaFold DB MCP — predicted protein structures.

WikiPathways MCP — open community pathway database.

MetaboLights MCP — EBI's metabolomics study repository.