"How to convert a PDF file into Markdown format" matching MCP servers:

MCP server to batch download open-access PDFs from PubMed Central (PMC), supporting PMCID/PMID lookup, parallel downloads, and download reports.

Enables AI agents to rank US healthcare organizations for clinical trial site feasibility, predicting patient accrual for a Graves' disease protocol using claims and registry data.

Enables natural-language querying of a mock legacy healthcare database and returns validated FHIR resources (Patient, Observation, Condition).

Enables genomic sequence analysis through the Evo 2 model, supporting DNA sequence scoring, embedding, generation, and variant effect prediction with multiple model checkpoints (7B, 40B, 1B parameters).

Enables variant annotation and effect prediction using the Ensembl VEP API, with support for batch and single queries.

An open source biomedical research agent that provides LLMs with 28 tools for drug discovery, protein analysis, literature search, medical imaging, omics, and sandbox execution, all running locally via Ollama and MedGemma.

MyChart MCP Server

TransBench is a translational research agent that takes free-text clinical observations, decomposes them into biological axes, generates falsifiable hypotheses grounded in PubMed evidence, and designs reproducible computational experiments with concrete datasets for Claude Science.

MCP server that turns a medRxiv DOI into clean markdown full text and provides free, relevance-ranked preprint search via Europe PMC.

Enables searching biomedical images (X-rays, CT/MRI, clinical photos, etc.) from the Open-i database using natural language queries, returning image results as Markdown links.

An MCP server that exposes a DICOMweb-compliant DICOM archive to AI assistants. It lets any MCP-capable client search studies, series and instances, inspect metadata, read Structured and Encapsulated PDF Reports, and render image frames — all through natural language.

Enables AI agents to turn clinical transcripts or audio recordings into structured SOAP notes, ICD-10/CPT billing codes, patient summaries, and visit summaries via SOAPNoteAPI.

Integrates AlphaFold DB and eight other biomedical data sources into MCP tools for variant clinical reporting, disease-target analysis, structural intelligence, and drug repurposing, with results persisted to a local SQLite knowledge graph.

MCP server for clinical charting with Claude (codename: Ratchet) - Enables Claude to document patient visits directly into Electronic Medical Records, reducing administrative burden for home health nurses.

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

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.

Integrates with FitSlot API to manage support tickets, provide chatbot assistance with FAQs, and analyze bioimpedance PDF documents with health metrics and personalized recommendations.

Enables biomedical research workflows via MCP, including experiment and document search, PDF text extraction, evidence retrieval, and validation with provenance tracking.

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.