"Extracting Orders from PDF Files" matching MCP servers:

Enables AI agents to search, filter, download files, and generate reports from the IGVF Data Portal using natural language commands.

Enables molecular generation, optimization, and analysis through NVIDIA MolMIM API. Supports generating drug-like molecules with desired properties, extracting molecular embeddings, and exploring chemical space around seed molecules.

An MCP server that wraps R scripts for microbiome and amplicon (16S/ITS) analysis, providing tools for alpha/beta diversity, differential abundance, networks, and more, with PNG/PDF outputs.

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

Enables protein sequence analysis and structure prediction by extracting ESM-2 embeddings and batch processing FASTA files via Docker. It provides tools for large-scale embedding extraction, job monitoring, and model management within an MCP-compatible environment.

MCP server that provides tools to query harmonized gene-disease validity data from the Gene Curation Coalition, supporting consensus and conflict detection for gene-disease assertions.

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

An MCP server for searching and accessing RNA sequencing datasets from the European Nucleotide Archive (ENA), supporting bulk, single-cell, and spatial transcriptomics with advanced filtering and download capabilities.

An MCP server that provides mouse genetics data from Mouse Genome Informatics (MGI), enabling LLM agents to query markers, mutations, alleles, phenotypes, and disease models.

Enables querying rare-variant, gene-based association results across ~1.2M individuals from 10 global biobanks, supporting phenome-wide scans, replication screens across ancestries, and candidate list evaluation for 44 harmonized traits.

An MCP server that provides tools for searching and fetching protein data from the UniProt database using the unipressed library.

Provides a Model Context Protocol server for accessing and querying biomedical data from BioThings services, including gene, variant, chemical, and taxon annotations.

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 standardized access to aging and longevity research data from the OpenGenes database, enabling AI assistants to query comprehensive biomedical datasets through SQL and structured interfaces.

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 querying genomics data from the Alliance of Genome Resources across model organisms including human, mouse, rat, zebrafish, fly, worm, yeast, and xenopus. Supports gene searches, disease associations, expression data, orthologs, phenotypes, and molecular interactions through natural language.

Enables AI assistants to access protein information directly from UniProt, allowing retrieval of protein names, functions, sequences, and organism data by accession number.

Enables searching and downloading Gene Expression Omnibus (GEO) data from NCBI, including datasets, series, samples, platforms, and profiles, through natural language queries.

Enables users to generate volcano plots by submitting jobs with input files and parameters, supporting local or Docker execution.

Enables AI assistants to query and analyze genomics data from the GTEx Portal through 25 specialized tools for gene expression analysis, eQTL/sQTL associations, and genetic variant lookups across 54 human tissue types.