"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.

Upload your raw DNA file from 23andMe, AncestryDNA, MyHeritage, FamilyTreeDNA, or any VCF -- and watch a team of AI agents fan out across 16+ public genomics databases, share discoveries with each other in real time, and produce a comprehensive health report. Everything runs on your machine. Nothing is uploaded anywhere.

A TypeScript MCP server for interacting with CDISC Define-XML 2.0 and 2.1 files, enabling users to load, search, and retrieve clinical data metadata including datasets, variables, and codelists. It supports local file processing with document caching and provides responses in both JSON and Markdown formats.

MCP server for MestReNova 15 that enables processing 1D NMR data, importing ChemDraw structures, running Mnova Verify, and writing back assignments with audit trails.

Enables design-correct, conversational analysis of NHANES public-use data by automating file discovery, merging, weight selection, pooling, survey variance estimation, and mortality-linked Cox models.

MCP server for connecting Claude Desktop to a local medical knowledge base with real-time file watching, enabling natural language interaction with medical documents.

Drive VMD headlessly from any MCP client to analyze structures and trajectories, and ray-trace publication-quality images with no display.

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.

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.

Enables controlling desktop ChemDraw from a terminal or MCP-connected assistant to create and edit native molecular structures, reaction schemes, styled figures, and batch exports, with editable CDXML and audit trails.

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 query free biomedical and pharmaceutical APIs for clinical trials, drug data, molecular structures, adverse events, and research literature.

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.

An MCP server that provides a toolbox for interacting with EPA SWMM stormwater models, enabling users to analyze model data and interpret results through LLM-driven tools. It assists stormwater modelers in understanding hydraulic systems and modeling behavior using natural language interfaces.

A local-first, model-agnostic MCP server that stores personal health data in a SQLite file and provides analysis-ready views for any AI client to log, retrieve, and reason over health records.

Provides access to Allen Institute for Neural Dynamics (AIND) metadata and data assets through MongoDB queries, aggregation pipelines, NWB file exploration, and AI-powered data summaries.

Enables AI assistants to perform quality control analysis on high-throughput sequencing data using FastQC and MultiQC. It supports single-file and batch processing of FASTQ/FASTA files and generates comprehensive, interactive summary reports.

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