"Chat with RAG (Retrieval-Augmented Generation)" matching MCP servers:

Enables AI coding assistants to query private academic paper collections via standard MCP tools, with hybrid retrieval, reranking, and inline citations.

Enables Claude to search a local hybrid retrieval index of research papers and ingest new PDFs, providing research-paper memory queryable directly through natural language.

Enables privacy-aware, deterministic, read-only chat analysis through tools for briefs, aggregate interaction signals, evidence-aware claim audits, and canonical resource discovery.

Enables creation and management of academic-paper knowledge bases from PDFs, including ingestion, semantic search with reranking, and document-level retrieval via MCP tools.

MCP server that integrates a 1200-paper RAG database with six tools to support research workflows across stages like hypothesis, experiment, statistics, and writing. It routes requests to specialized skills and real-time frontier searches to provide evidence-grounded research mentoring.

Exposes hybrid document retrieval and evaluation tools from retrieval-lab via MCP, including search_documents, corpus_info, run_evaluation, and search_my_repos, with wire-level conformance tests.

A local MCP server for evidence-safe academic citation workflows, including verified-reference retrieval, Zotero duplicate detection and import, and Word export via Pandoc with zotero.lua.

Enables discovering and independently validating scholarly metadata from extracted research text using Crossref, OpenAlex, DataCite, and optional read-only Zotero checks, returning ranked and verified reference candidates.

An MCP server that enables advanced CSV analysis and data visualization using Google's Gemini AI and Plotly. It allows users to perform exploratory data analysis, generate interactive charts, and conduct complex reasoning on tabular data.

A comprehensive Model Context Protocol (MCP) server providing advanced access to the UniProt protein database.

A local-first paper RAG server that enables searching and managing academic PDFs via MCP tools, supporting metadata enrichment and citation graphs.

Enables passage-level semantic search over a Zotero library by extracting, chunking, and embedding PDF text using Gemini and ChromaDB. It provides MCP tools to perform topical searches and retrieve specific document passages with surrounding context.

A comprehensive Model Context Protocol (MCP) server for accessing the SureChEMBL chemical patent database.

A comprehensive Model Context Protocol (MCP) server that provides access to the Ensembl REST API for genomic data, comparative genomics, and biological annotations.

Model Context Protocol server for accessing Reactome pathway and systems biology data.

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.

A comprehensive Model Context Protocol (MCP) server for accessing Human Protein Atlas data, providing information about protein expression, subcellular localization, pathology, and more.

A comprehensive Model Context Protocol server for accessing Gene Ontology (GO) data, enabling AI systems to perform ontology-based analysis, gene annotation research, and functional enrichment studies.

A production-ready Model Context Protocol (MCP) server that provides comprehensive access to the BioOntology API for searching, annotating, and exploring over 1,200 biological ontologies.

A comprehensive Model Context Protocol (MCP) server that provides access to the AlphaFold Protein Structure Database through a rich set of tools and resources for protein structure prediction analysis.