"Official tool for reading and analyzing PDF files from MCP" matching MCP servers:

Provides an MCP interface to the ROBOT command-line tool for OWL ontology editing, enabling operations like merging, reasoning, and conversion via natural language.

MCP server for the STRING protein–protein interaction database, hosted by STRING at mcp.string-db.org. Adapted for LLM grounding: responses are size-limited and include metadata and notes on interpretation and next steps. Tools cover identifier resolution, interaction networks and evidence, functional and PPI enrichment, and sequence similarity search.

A stateless, deterministic Bio-Robotics Core Engine converting biological data (UniProt API) to G-code.

MCP server for biopharma software infrastructure offering FDA 21 CFR Part 11 audit trails, CDISC SDTM/Allotrope data exports, 4PL dose-response curve fitting, and HIPAA PII/PHI redaction through 10 Zod-validated tools.

An MCP server for High-Throughput Screening (HTS) assay calculations across sub-cellular, cellular, tissue, and organism biological tiers, enabling local-first bioassay analysis.

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.

Enables users to resolve regulatory entities, query and analyze biological interactions, inspect evidence, export reproducible network data, and download official compressed source files on demand through an online-first, read-only service.

Enables interaction with MGnify metagenomics resources and tools through the Model Context Protocol. Provides access to MGnify's API for querying and analyzing metagenomic datasets and related biological information.

Retrieve genomic data from EGA, ENA, ENCODE, GEO and NCBI, read bounded regions from indexed BAM/CRAM, VCF and bigWig files, and query source-attributed reference evidence. Runs locally with 23 MCP tools. MIT-licensed; research use.

Enables AI assistants to query genetic variant data, gene constraints, and population genetics information from the gnomAD (Genome Aggregation Database) through its GraphQL API. Supports searching for genes and variants, retrieving constraint scores, analyzing population frequencies, and accessing genomic coverage data.

Enables MCP clients and the cheminfo chat to call one catalog of tools while carrying produced structures, reaction schemes, spectra and files beside the answer rather than through the model. It provides tool listing, tool invocation, and stateless Streamable HTTP MCP endpoints.

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

Enables building and analyzing signalling networks from interaction databases through a Model Context Protocol server.

Official public, read-only Helena Bioinformatics MCP for source-cited answers about the company and its published products.

Enables searching and retrieving cancer-genomics projects, cases, and genomic data files — including TCGA, TARGET, and CPTAC — via keyless, open-access metadata tools. Supports filtering by primary site, project, or data category, and can route plain-English questions to the right tool automatically.

Enables querying of the Monarch Initiative biomedical knowledge graph for genes, diseases, phenotypes, and their associations through natural language or direct tool calls.

An MCP server that provides access to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, offering 30 tools for searching and analyzing biological data like pathways, genes, and compounds. It supports integration with LangChain and Ollama to enable LLMs to interact with comprehensive genomic and chemical datasets.

Unified genomic track, peak, and sequence retrieval tool for ENCODE, ChIP-Atlas, ReMap, GEO, and SRA/ENA with unified metadata, resolved DOI/PMID provenance, and direct FASTQ download without SRA toolkit.

This server provides access to InterPro protein family, domain, and functional-site classification data from EBI. It allows querying protein annotations through natural language or direct tool calls.

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

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.

Folklore MCP 2.0.0: 11 public tools for ACMG/AMP variants, genes and literature. A Folklore API key adds 18 tools, 29 in total, for cases, authorized source files, original JSON/PDF results and six JSON views. Use a Bearer header at the same hosted endpoint. Processing follows account subscription limits or available credits.

Validates the physical and chemical plausibility of ligand–protein docking poses using the PoseBusters tool.

Enables searching and retrieving curated mathematical models of biological systems from BioModels, including metadata, source publications, and downloadable model files in SBML, BioPAX, and other formats, with querying by pathway, disease, organism, gene, or author.

Enables AI assistants to query VCF files through MCP tools that summarize variants, identify pathogenic and carrier variants, interpret pharmacogenomic results, and determine APOE status, with web app and Claude Desktop support.

Framework for building bioengineering automation tools that AI assistants can call via the Model Context Protocol, handling server registration and tool discovery automatically.

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.

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 language models to search biomedical literature, fetch sequences, and follow links across Entrez databases through eleven read-only tools wrapping the nine NCBI Entrez E-utilities. It handles URL building, pacing, redirects, response caps, and API-key redaction so queries can be answered without a browser or scraping.