"Searching for publications by user 'modelcontextprotocol' on MCP" matching MCP servers:

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.

Enables querying the EMBL-EBI catalog of published polygenic scores through read-only tools that search scores, traits, publications, performance metrics, sample sets, cohorts, and releases, and that trace GWAS studies and resolve ontology and ancestry identifiers. It also lists and downloads the associated scoring-file and metadata files from the catalog's FTP site.

Enables AI-driven pharmacogenomic analysis by querying structured genetic variant, drug response, and disease risk data. Supports natural language questions about medications, traits, and health risks based on user genome data, with privacy-first local execution.

Enables AI assistants to query and retrieve microbial nomenclature data from the SeqCode Registry through its public REST API. Provides 18 tools for names, genomes, type genomes, register lists, publications, authors, journals, subjects, strains, and full-text search, with pagination and status filtering.

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 searching a manually curated database of stable macromolecular protein complexes by protein or complex name, gene, GO term, or biological process, and fetching individual records by accession to retrieve subunits with UniProt identifiers, biological roles, and stoichiometry. Complements UniProt, IntAct, and STRING, and can be used keyless over a hosted gateway endpoint or run locally over stdio.

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 life-science research by providing search and retrieval across linked publications, clinical trials, drugs, genes, regulatory approvals, and patents through MCP clients.

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

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

Enables in-chat scientific viewers for molecular structures, sequence alignments, and slide images, plus data tools for searching structures, fetching sequences, aligning them, and drafting NGS analysis plans.

A specialized MCP server for Metal-Organic Framework research that provides tools for database searching, structural optimization, and energy calculations via ASE. It enables scientific workflows by allowing users to interact with MOF data and perform chemical simulations through a standard SSE interface.

Enables searching cryo-EM density maps in EMDB and raw datasets in EMPIAR, with filtering by resolution, keyword, and cross-referencing between the two databases.

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

Enables searching EBI BioStudies, a keyless database of biological study descriptions, by keyword and retrieving full metadata for a single study by accession, including title, abstract, release date, and link counts. Results tie studies across EBI archives such as ArrayExpress and PRIDE, so agents can locate and inspect study records without authentication.

Enables searching and retrieving curated mathematical models of biological systems from BioModels, including metadata, source publications, and downloadable model files in SBML, BioPAX, and other formats, with querying by pathway, disease, organism, gene, or author.

Enables searching and retrieving expert-curated biochemical reactions from the Rhea database by compound name, ChEBI id, EC number, keyword, or Rhea id, returning balanced plain-text reaction equations alongside EC, ChEBI, UniProt, and PubMed cross-references.

Enables evidence-traceable annotation of human and mouse single-cell data by resolving ontology terms, searching versioned marker and reference-atlas indexes, ranking and auditing candidate cell types, and exporting sealed decision bundles with provenance.

Enables querying and retrieving cell line records from the Cellosaurus knowledge base via its REST API, including searching, fetching by accession, and accessing release information.

Enables searching for academic papers and preprints across multiple platforms including Semantic Scholar, arXiv, PubMed, and CrossRef. It provides access to research records, DOI lookups, and journal metadata through a unified interface deployed on Cloudflare Workers.

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 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.

Enables interaction with the CEDAR metadata repository, including fetching templates, searching BioPortal ontology terms, and managing template instances.

Enables AI-assisted molecular biology experiment design with tools for qPCR primer design, cloning strategy optimization, TaqMan probe design, and multiplex compatibility analysis.

An MCP server that enables AI coding assistants to interact with Rosetta, PyRosetta, and Biotite for running RosettaScripts, validating XML, translating between Rosetta and Biotite, scoring structures, and querying documentation.