"Linux-compatible version of Cursor" matching MCP servers:

Control PyMOL from Cursor via natural language. Enables describing molecular structures and styles in plain language to execute PyMOL commands through XML-RPC.

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.

Enables querying and accessing hivtools data through a REST API and MCP-compatible tools.

Enables keyless lookup of marine species and genus names, retrieval of full taxonomic lineages by AphiaID, and common vernacular names across languages via MCP tools.

Grounds gene-nomenclature work in the HUGO Gene Nomenclature Committee (HGNC) dataset, enabling resolution of gene symbols and IDs to canonical HGNC identifiers, plus cross-references and batch operations.

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.

MCP server that exposes the UniProt REST API to LLM clients, enabling search and retrieval of protein data via tools like search_uniprotkb, get_entry, and map_ids.

Enables discovery, inspection, and cross-referencing of Protein Data Bank structures through three RCSB APIs: search, data, and sequence coordinates.

Enables editing and querying of Gene Ontology Causal Activity Models (GO-CAMs) through the Barista API. Supports model creation, individual and fact management, evidence addition, and causal pathway construction for biological knowledge representation.

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.

MCP server for single-cell lineage tracing analysis, enabling conversational reconstruction, visualization, and heritability analysis of lineage trees using Cassiopeia, pycea, and treedata.

Enables gene set enrichment analysis using the Enrichr API across hundreds of gene set libraries including Gene Ontology, pathways, diseases, tissues, drugs, and transcription factors. Returns only statistically significant results for interpretation.

Converts natural language queries into Cypher queries against the NASA GeneLab Knowledge Graph, enabling AI-assisted analysis of spaceflight experiments and their biological effects.

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.

Run real bioinformatics from your AI agent on your own GPUs: MMseqs2 homology search, ESMFold structure prediction and sequence tools for Claude, Cursor and Codex. GPU-aware scheduling for shared machines, fail-fast input checks, background jobs, agent-friendly results and provenance for every run.

Enables the generation, mutation, and evolution of DNA and protein sequences using various evolutionary models and phylogenetic algorithms. It supports realistic next-generation sequencing read simulation and population-level evolutionary tracking for bioinformatics research and testing.

Enables natural language control of UCSF ChimeraX for protein structure visualization, editing, and analysis through MCP clients.

A Model Context Protocol (MCP) server that provides access to the Protein Data Bank (PDB) - the worldwide repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies.

Provides 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.