"A resource for finding 3D models" matching MCP servers:

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.

MCP server offering verified bioinformatics tools for sequence utilities and statistics, backed by BioPython/scipy. Enables AI agents to perform accurate GC content, translation, ORF finding, motif scanning, and statistical tests through natural language.

An MCP server for querying the KEGG bioinformatics database, providing tools, resource templates, and guided prompts for pathways, genes, compounds, and more.

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

Enables AI agents to conversationally interact with genomics research networks for data analysis and discovery across multiple Omics AI Explorer platforms. It provides tools for exploring data collections, examining table schemas, and executing SQL queries against datasets like Viral AI and Neuroscience AI.

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.

An MCP server that exposes the KEGG REST API — pathways, genes, compounds, reactions, enzymes, diseases, drugs, modules, orthology, glycans, and BRITE hierarchies, with cross-database linking. Provides 34 tools and 8 resource templates.

Enables AI agents to resolve genes, diseases, chemicals, variants and species to normalized ids, search ~36M PubMed abstracts and PMC full texts by free text or entity, and retrieve the machine-extracted relations between them with the supporting sentences and PMIDs. Supports auditing individual relations with full evidence passages and pulling per-article entity annotations with character offsets.

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 users to search and retrieve 3D cryo-EM and electron-tomography density maps by keyword or entry ID, returning details such as resolution, structure-determination method, sample, and release date.

Enables looking up genes, fetching sequences, predicting variant consequences, finding orthologs, and cross-database xrefs via Ensembl REST API through MCP.

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.

Enables querying BindingDB for measured protein/small-molecule binding affinities, including finding ligands that bind a protein, protein targets for a compound, and affinities from PDB structures.

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.

🔍 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

This server enables multi-agent conversations for interacting with Cirro's biological data platform through its OpenAPI interface, auto-generated using AG2's MCP builder.