"A guide to creating 3D models in Blender" matching MCP servers:

Enables 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).

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

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.

Connects 3D Slicer with AI assistants through the Model Context Protocol, enabling medical image processing and scene manipulation using natural language.

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.

A Model Context Protocol server that enhances language models with protein structure analysis capabilities, enabling detailed active site analysis and disease-related protein searches through established protein databases.

A Model Context Protocol server providing programmatic access to 3D protein structural data from RCSB PDB, PDBe, and UniProt, enabling search, retrieval, comparison, and analysis of protein structures.

Enables automated cell type annotation in scRNA-seq analysis using CellTypist models, with tools for listing, downloading, training, and annotating cell types via natural language.

Searches UniProt by protein name to find accession numbers and retrieves detailed protein structure information from AlphaFold, including direct links to 3D structural predictions.

Provides access to AlphaFold predicted protein 3D structures from EBI, enabling retrieval of prediction metadata, summaries, annotations, and UniProt data.

Integrates GROMACS molecular dynamics simulations with VMD visualization, enabling setup, execution, analysis, and 3D visualization of molecular dynamics workflows through natural language.

An MCP server that enables language models to fetch protein information from the UniProt database, including protein details, sequences, functions, and structures.

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.

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

Enables LLMs and AI agents to query a biomedical knowledge graph stored in RedisGraph, with tools for concept search, synonym enrichment, and study variable discovery through semantic relationships.

🔍 Enable AI assistants to search and access bioRxiv papers through a simple MCP interface. The bioRxiv MCP Server provides a bridge between AI assistants and bioRxiv's preprint repository through the Model Context Protocol (MCP). It allows AI models to search for biology preprints and access their

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.

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.

Provides direct SQL access to a locally hosted Reactome database, enabling schema discovery, guarded read-only queries, and ergonomic helpers over the full relational schema.

Renders interactive 2D molecular structure diagrams from SMILES notation and computes molecular properties like molecular weight, LogP, and TPSA, directly in the chat.