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qualityD
maintenanceControl 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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"Using Cursor to Handle Documentation During a Commit" matching MCP servers:
- AlicenseAqualityCmaintenanceEnables genomic sequence analysis through the Evo 2 model, supporting DNA sequence scoring, embedding, generation, and variant effect prediction with multiple model checkpoints (7B, 40B, 1B parameters).62LGPL 3.0
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- AlicenseAqualityCmaintenanceProvides direct SQL access to a locally hosted Reactome database, enabling schema discovery, guarded read-only queries, and ergonomic helpers over the full relational schema.9MIT
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- 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
- AlicenseAqualityFmaintenanceAn 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.1911218MIT
- AlicenseAqualityDmaintenanceAn MCP server that provides tools for searching and fetching protein data from the UniProt database using the unipressed library.2MIT
- AlicenseAqualityCmaintenanceMCP server for single-cell lineage tracing analysis, enabling conversational reconstruction, visualization, and heritability analysis of lineage trees using Cassiopeia, pycea, and treedata.18MIT
- AlicenseAqualityCmaintenanceConnects 3D Slicer with AI assistants through the Model Context Protocol, enabling medical image processing and scene manipulation using natural language.338MIT
- FlicenseAqualityDmaintenanceProvides access to EMBL-EBI bioinformatics data including InterPro domains, Pfam families, protein features, and taxonomy through a unified tool.11
- AlicenseAqualityAmaintenanceA stateless, deterministic Bio-Robotics Core Engine converting biological data (UniProt API) to G-code.6MIT
- AlicenseAqualityDmaintenanceA high-performance MCP server that gives LLMs access to 25 biomedical tools federated across 50+ upstream APIs for genes, variants, drugs, diseases, literature, clinical trials, and structural biology.25672MIT
- AlicenseAqualityDmaintenanceEnables 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.6BSD 2-Clause "Simplified"
- AlicenseBqualityDmaintenanceProvides a programmatic interface to the Genome Aggregation Database (gnomAD) API across versions v2.1.1, v3.1.2, and v4.1.0. It enables users to query gene metadata, variant information, population frequencies, and ClinVar data through a unified schema.126Apache 2.0
- FlicenseBqualityDmaintenanceA production-ready Model Context Protocol (MCP) server that provides comprehensive access to the BioOntology API for searching, annotating, and exploring over 1,200 biological ontologies.109
- FlicenseBqualityCmaintenanceEnables protein structure and sequence searches using FoldSeek, with support for multiple databases, automatic model downloads, and structured job management.5
- FlicenseBqualityFmaintenanceA comprehensive Model Context Protocol server providing access to over 110 million chemical compounds with extensive molecular properties, bioassay data, and chemical informatics tools from the PubChem database.3046
- AlicenseBqualityCmaintenanceAllows to retrieve information about an AnnData object via MCP using the read_lazy function from anndata.37MIT
- AlicenseBqualityAmaintenanceEnables AI coding agents to search academic papers, resolve biomedical entities, mine relations, and traverse citation graphs using Semantic Scholar and PubTator3, with local caching for reproducibility.11MIT
