F
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qualityD
maintenanceFramework for building bioengineering automation tools that AI assistants can call via the Model Context Protocol, handling server registration and tool discovery automatically.
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"Browser automation and control for Codex CLI" matching MCP servers:
- AlicenseBqualityDmaintenanceProvides comprehensive access to the UCSC Genome Browser API, enabling queries of genomic data, DNA sequences, gene annotations, variants, and metadata across multiple species and assemblies.126MIT
- -license-quality-maintenanceThis server enables multi-agent conversations for interacting with Cirro's biological data platform through its OpenAPI interface, auto-generated using AG2's MCP builder.
Copick MCP Serverofficial
Alicense-qualityCmaintenanceEnables read-only exploration of Copick cryo-ET projects and discovery/validation of copick CLI commands for building processing pipelines.MIT- Alicense-qualityCmaintenanceEnables AI agents to control RELION 5.x cryo-EM structure determination software through natural language, providing 23 tools for the complete single-particle analysis pipeline.2MIT
- Alicense-qualityCmaintenanceMCP server for biological protein design, folding, and affinity prediction using Refua tools, with optional support for ADMET, clinical simulation, preclinical planning, wet-lab automation, and more.MIT
- Flicense-qualityBmaintenanceA terminal-based bioinformatics CLI chat tool that integrates Ensembl VEP, NCBI ClinVar, an MCP server layer, and OpenRouter's NVIDIA Nemotron 3 Ultra model to provide variant consequence and clinical significance lookups with clear summaries in a Rich-powered CLI.
- Flicense-qualityDmaintenanceControl PyMOL from Cursor via natural language. Enables describing molecular structures and styles in plain language to execute PyMOL commands through XML-RPC.1
- Flicense-qualityDmaintenanceA Model Control Protocol implementation for SAMtools, providing a standardized interface for working with SAM/BAM/CRAM files.
- AlicenseAqualityDmaintenanceA 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.88MIT
- AlicenseAqualityAmaintenanceAn MCP server for querying the KEGG bioinformatics database, providing tools, resource templates, and guided prompts for pathways, genes, compounds, and more.343MIT
- AlicenseAqualityDmaintenanceEnables AI assistants to query the Ubergraph biomedical ontology SPARQL endpoint with tools for custom SPARQL queries, term lookup, search, and hierarchy traversal.4MIT
- AlicenseAqualityCmaintenanceEnables variant annotation and effect prediction using the Ensembl VEP API, with support for batch and single queries.91MIT
- AlicenseAqualityDmaintenanceEnables natural language control of UCSF ChimeraX for protein structure visualization, editing, and analysis through MCP clients.393MIT
- AlicenseBqualityDmaintenanceProvides seamless access to UniProtKB protein database, enabling queries for protein entries, sequences, Gene Ontology annotations, full-text search, and ID mapping across 200+ database types.52MIT
- AlicenseBqualityCmaintenanceProvides comprehensive BioPython capabilities for biological sequence analysis, alignment, database access (GenBank, UniProt, PubMed), protein structure analysis, and phylogenetics through a Model Context Protocol interface for AI-assisted bioinformatics workflows.323MIT
- FlicenseBqualityDmaintenanceA comprehensive Model Context Protocol (MCP) server for accessing the STRING protein interaction database. This server provides powerful tools for protein network analysis, functional enrichment, and comparative genomics through the STRING API.64
- AlicenseBqualityDmaintenanceSearch PubMed for articles matching the query.167MIT
- AlicenseBqualityDmaintenanceServer to search PubMed (PubMed is a free, online database that allows users to search for biomedical and life sciences literature). I have created on a day MCP came out but was on vacation, I saw someone post similar server in your DB, but figured to post mine.147MIT
- FlicenseBqualityDmaintenanceEnables AI assistants to query genetic variant data, gene constraints, and population genetics information from the gnomAD (Genome Aggregation Database) through its GraphQL API. Supports searching for genes and variants, retrieving constraint scores, analyzing population frequencies, and accessing genomic coverage data.910