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"Understanding Cursor or Cline Context in Long-term Memory Systems" matching MCP servers:

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    Control PyMOL from Cursor via natural language. Enables describing molecular structures and styles in plain language to execute PyMOL commands through XML-RPC.
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    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.
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    MIT
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    Enables AI assistants to query the Ubergraph biomedical ontology SPARQL endpoint with tools for custom SPARQL queries, term lookup, search, and hierarchy traversal.
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    MIT
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    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.
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    MIT
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    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.
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    MIT
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    A bridge connecting AI agents to NCBI's PubMed database through the Model Context Protocol, enabling seamless searching, retrieval, and analysis of biomedical literature and data.
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    Apache 2.0
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    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.
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    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.
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    ▎ 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.
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    Provides seamless access to the Protein Data Bank in Europe (PDBe) API and search capabilities, enabling AI clients to query protein structures, perform advanced searches, and retrieve structural biology data.
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    Apache 2.0
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    Provides LLMs with structured access to critical biomedical databases including PubTator3 (PubMed/PMC), ClinicalTrials.gov, and MyVariant.info through the Model Context Protocol.
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    Provides 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.
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    MIT