"Understanding File Structures" matching MCP servers:

Enables AI assistants to clean PDB structures and run initial-stage energy relaxation for biomolecular modeling. It provides a structured workflow for preparing structures before production molecular dynamics or coarse-graining pipelines.

An 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.

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

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 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.

Provides programmatic access to AlphaFold protein structure predictions and UniProt data, enabling users to retrieve protein structures, summaries, and annotations through natural language.

Enables AI agents to search and retrieve compounds, drugs, diseases, pathways, genes, enzymes, glycans, modules, and KO entries; fetch full parsed flat-file entries by ID; and list database contents through keyless REST tools.

Enables LLM agents to design proteins, predict structures, score interfaces, and run molecular dynamics simulations through a unified interface.

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.

Provides chemical informatics endpoints for converting between chemical names and SMILES, processing molecule structures, and comparing molecules, with MCP compatibility.

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.

Enables querying and retrieving experimental protein structures from the RCSB Protein Data Bank, including text search, full entry records, polymer entities, ligands, and assemblies.

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

Enables interaction with the RCSB Protein Data Bank to search, analyze, and visualize protein structures. It provides specialized tools for downloading coordinate files and performing structural modifications like residue mutations and metal atom replacements.

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

Enables RNA structure analysis, sequence evaluation, and inverse design using geometric deep learning models. Supports both quick computational analysis and long-running batch processing for generating RNA sequences that fold into target structures.

Enables in-chat scientific viewers for molecular structures, sequence alignments, and slide images, plus data tools for searching structures, fetching sequences, aligning them, and drafting NGS analysis plans.

Enables searching, retrieving, and downloading protein structure data from the RCSB Protein Data Bank. Supports intelligent protein structure search, comprehensive data retrieval, and multiple file format downloads for bioinformatics research.

BioMCP is an open-source MCP server that connects any AI assistant to 15 open bioinformatics databases with zero configuration. It provides 23 tools for literature, sequences, BLAST, structures, enrichment, annotations, genomes, interactions, variants, domains, compounds, and single-cell data.