Enzyme

Enzyme is an MCP (Model Context Protocol) server designed to index, analyze, and enable semantic search of large knowledge bases such as Obsidian vaults, markdown file collections, and Readwise exports. It compiles content into a concept graph in seconds, exposing tools like 'init', 'petri', and 'catalyze' for initializing, visualizing, and conducting advanced thematic queries through MCP-compatible AI assistants (e.g., Claude, Cursor, Windsurf). Enzyme works locally and is ideal for engineers, researchers, writers, and teams who want high-performance, privacy-first semantic search and context-aware knowledge management across personal or team knowledge repositories. It integrates natively with Obsidian, supports PKM workflows, and enables deep question answering and cross-document insight discovery—without needing to maintain conversation history or rely on runtime analysis.