"Using the Structured app for organization or productivity" 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 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.

An MCP server that provides tools for searching and fetching protein data from the UniProt database using the unipressed library.

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

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

Provides standardized access to aging and longevity research data from the OpenGenes database, enabling AI assistants to query comprehensive biomedical datasets through SQL and structured interfaces.

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

MCP server for querying the GWAS Catalog (EBI/NHGRI), a curated catalog of genome-wide association studies. It enables AI agents to search and retrieve study data via natural language or direct tool calls.

Enables querying of the Monarch Initiative biomedical knowledge graph for genes, diseases, phenotypes, and their associations through natural language or direct tool calls.

Enables AI agents to query the fission yeast PomBase database for gene summaries, GO annotations, phenotypes, orthologs, domains, and interactions via structured API calls.

Enables querying and retrieving bacterial and viral genomic data, features, antimicrobial resistance, and epitopes from the BV-BRC API using natural language.

Enables querying the Human Protein Atlas data using natural language or direct MCP tools, with keyless access via the Pipeworx gateway.

Validates the physical and chemical plausibility of ligand–protein docking poses using the PoseBusters tool.

MCP server for querying the EBI PRIDE Archive, a proteomics (mass-spectrometry) data repository, through natural language or direct tool calls.

Enables AI agents to resolve scientific (Latin binomial) names to Open Tree of Life taxon IDs, retrieve full taxonomic details, synonyms, and ancestor lineages, and find the most recent common ancestor of up to 10 taxa within the synthetic tree of life. Runs keylessly over a hosted gateway endpoint or locally via npx.

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 LLMs to run rule-based molecular interaction simulations using the Kappa language through the Kappybara package. Returns simulation results as CSV data for analysis of biochemical systems and molecular binding dynamics.

Enables AI assistants to query VCF files through MCP tools that summarize variants, identify pathogenic and carrier variants, interpret pharmacogenomic results, and determine APOE status, with web app and Claude Desktop support.

Provides a natural language interface for single-cell RNA-Seq analysis using the decoupleR framework. It enables users to perform biological pathway inference, data clustering, and visualization through MCP-compatible AI clients.

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