"Tools and applications for reading PDF files" matching MCP servers:

Provides a collection of MCP servers for computational chemistry tasks including molecular generation and retrosynthesis. Also offers property prediction and molecule pricing capabilities.

Enables deep probabilistic analysis of single-cell omics data using scvi-tools through natural language. Supports SCVI for scRNA-seq analysis, SCANVI for cell type annotation, TOTALVI for multi-modal RNA/protein data, and PEAKVI for scATAC-seq analysis.

A specialized MCP server for Metal-Organic Framework research that provides tools for database searching, structural optimization, and energy calculations via ASE. It enables scientific workflows by allowing users to interact with MOF data and perform chemical simulations through a standard SSE interface.

Enables searching cryo-EM density maps in EMDB and raw datasets in EMPIAR, with filtering by resolution, keyword, and cross-referencing between the two databases.

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.

Provides programmatic access to curated SNP data by trait, enabling LLM-powered applications to search, interpret, and discover genetic variants.

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 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.

MCP server for querying BV-BRC biological data, submitting analysis jobs (assembly, annotation, BLAST, etc.), and managing workspace files via natural language.

Enables Claude Code to interact with a TACC or SLURM HPC cluster for bioinformatics pipelines, allowing job management, log reading, file browsing, remote script execution, and job submission through natural language.

A Model Control Protocol implementation for SAMtools, providing a standardized interface for working with SAM/BAM/CRAM files.

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.

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.

Enables AI-assisted molecular biology experiment design with tools for qPCR primer design, cloning strategy optimization, TaqMan probe design, and multiplex compatibility analysis.

Provides local DNA/RNA sequence analysis tools (composition, reverse complement, translation, ORF enumeration, motif scanning) via MCP for agent workflows.

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

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

Enables AI assistants to query the Ubergraph biomedical ontology SPARQL endpoint with tools for custom SPARQL queries, term lookup, search, and hierarchy traversal.

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 framework that integrates Brain-Computer Interface technology with the Model Context Protocol to enable real-time neural signal processing and AI-powered interactions for healthcare, accessibility, and research applications.