"Buy Me A Coffee" matching MCP servers:

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.

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.

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 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.

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.

Guides researchers, including those new to BPP, from raw sequence data to a validated control file that has passed a short test run. Wraps BPP command-line tools without running long analyses itself.

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

Enables analysis of bulk RNA-seq data using natural language queries, executing R and Python in a Docker container with automatic sample anonymization and privacy controls.

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.

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.

MCP server and Claude Plugin for a full ENCODE Project genomic data and analysis toolkit — search, download, track, and analyze functional genomics experiments

Enables AI assistants to rapidly gather and synthesize structural, chemical, conservation, and literature data about protein binding pockets for drug-target triage. Useful as a reconnaissance step before computational binder design.

MCP server that provides tools for querying the Human Phenotype Ontology (HPO) including term lookup, hierarchy exploration, cross-ontology mappings, and gene-phenotype-disease associations, all grounded in a local SQLite database for fast offline lookups.

Enables LLM agents to search EMDB cryo-EM maps, look up UniProt proteins, compute ESM-2 sequence embeddings, retrieve cryo-EM maps from a protein sequence via a two-tower model, and search GEO DNA-methylation arrays, all through typed tools with structured output. Ships with a 40-question evaluation harness that runs Claude as the MCP client.

Enables users to search multiple public life-science data repositories (GEO, ENA, CELLxGENE, PRIDE, DataCite) with a single query, returning a unified ranked list of datasets with ontology-expanded terms and per-source error reporting.

Enables agents to search a public PubMed-derived corpus by natural language or identifiers and to retrieve publication details while traversing bounded citation and semantic literature graphs.

Enables researchers to query public ENA and BioSamples genomics data in plain English through any MCP client, including counting records, searching samples, retrieving sample details, and checking metadata quality against project requirements.

Integrates AlphaFold DB and eight other biomedical data sources into MCP tools for variant clinical reporting, disease-target analysis, structural intelligence, and drug repurposing, with results persisted to a local SQLite knowledge graph.

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.

Provides a Model Context Protocol server for accessing and querying biomedical data from BioThings services, including gene, variant, chemical, and taxon annotations.

Enables MCP clients to discover and call typed tools for protein backbone design, sequence design, complex folding, and binder design via BioNeMo NIMs, with a deterministic simulator by default and optional live routing.

Provides access to EMBL-EBI bioinformatics data including InterPro domains, Pfam families, protein features, and taxonomy through a unified tool.

A stateless, deterministic Bio-Robotics Core Engine converting biological data (UniProt API) to G-code.

Enables AI-powered genomic variant analysis including variant impact prediction, regulatory element discovery, and batch variant scoring. Currently operates in mock mode as a proof-of-concept awaiting the public release of Google DeepMind's AlphaGenome API.

Read-only access to a curated, evidence-labelled corpus of mTOR research: studies, entities, signed pathway relations with supporting and conflicting evidence, and open questions.

▎ Provides 32 tools for plant-genomics locus lookup across 11 free public backends (Ensembl Plants, Phytozome, UniProtKB, Europe PMC, QuickGO, NCBI BLAST, Gramene, KEGG, STRING-DB, ATTED-II, BAR). Takes a TAIR-style locus plus optional organism and returns gene metadata, functional/pathway annotation, interactions, co-expression, and literature — in single-locus, batch, and cross-source synthesis.

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

A Model Context Protocol server providing LLMs with access to the Ensembl genomics database, enabling AI assistants to query gene information, sequences, variants, and other genomic data across multiple species.

Enables AI agents to conversationally interact with genomics research networks for data analysis and discovery across multiple Omics AI Explorer platforms. It provides tools for exploring data collections, examining table schemas, and executing SQL queries against datasets like Viral AI and Neuroscience AI.