Enzyme Enzyme helps you develop deeper convictions through your notes by focusing on atomic note-taking and organic knowledge evolution. Unlike traditional note-taking apps, Enzyme treats your knowledge as a living, evolving graph that you can interact with, visualize, and extract insights from.
Setting Up Your Vault
After installing Enzyme, the first step is connecting it to your knowledge vault:
- Open Enzyme and click “Connect Vault” in the welcome screen
- Select your existing Obsidian vault or create a new one
- Enzyme will begin indexing your notes, identifying entities, and building connections
Enzyme works best with plaintext notes that use tags, but don’t worry if your current system is different—we’ll help you adapt as you go.
Understanding the Graph Interface
This isn’t just a static visualization—it’s a playground for your ideas:
- Tags and Entities appear as nodes and might represent key concepts, people, or themes in your notes
- Connections show relationships between entities based on co-occurrence in your notes
- Timeline view displays when notes were created, helping you track the evolution of ideas
The graph is designed to reveal patterns in your thinking that might otherwise remain hidden in folders or chronological lists.
Adding Notes Through Entity Interaction
Enzyme makes capturing thoughts around specific entities effortless:
- Click on any entity in the graph to create a new note mentioning it
- Drag horizontally on an entity to adjust how prominently it features in your note
- Connect multiple entities by selecting them before creating a note
This approach encourages atomic note-taking—capturing discrete thoughts rather than lengthy documents—which makes your knowledge more flexible and reusable.
Generating Recipes: AI-Powered Insight Extraction
When you’re ready to extract insights from your notes, Enzyme’s recipe generator becomes invaluable:
- Select one or more entities of interest in your graph
- Click “Generate Recipe”
- Enzyme will extract the neighborhood of notes around these entities
- The AI analyzes these notes and synthesizes key insights, patterns, and questions
Recipes aren’t just summaries—they’re jumping-off points for deeper exploration, writing projects, or decision-making.
Scheduled Digests: Building Reflection Habits
Disclaimer: this is a feature that’s still under active development.
Enzyme helps you develop regular reflection habits through scheduled digests:
- Set up a digest schedule (daily, weekly, or custom)
- Choose which tags or entities to include
- Enzyme will generate a personalized digest at your specified times
- Each digest highlights new connections, emerging patterns, and suggested areas for exploration
This feature is particularly valuable for ADHD thinkers who benefit from structured prompts for reflection without having to remember to do it in the moment.
Using Enzyme as a Context Server
One of Enzyme’s most powerful features is its ability to serve as a context provider for other applications:
- As long as the Enzyme app is open, it maintains an index of your knowledge
- This index is available to other applications that support the Model Context Protocol (MCP)
- Compatible apps include Claude Desktop, Cursor, and other MCP-enabled tools
This means you can access your knowledge base from within conversations with AI assistants without manually copying and pasting content.
See this post for a more detailed guide on using Enzyme with Claude Desktop.
Developing Deeper Convictions
Unlike tools focused solely on organization or retrieval, Enzyme is designed to help you develop deeper convictions through your notes:
- By connecting ideas across time, you build on previous thoughts rather than starting fresh
- The visual nature of the graph helps you see how concepts relate to each other
- AI-generated recipes highlight patterns you might miss when looking at notes individually
- The ability to track how your thinking evolves prevents you from “moving in circles”
Community and Support
Join our growing community of knowledge enthusiasts:
- Share your Enzyme workflows in our Discord server
- Contribute to our open discussions about the future of personal knowledge management
We believe that the best knowledge tools respect existing workflows while gently encouraging better habits. Our community reflects this philosophy.
Remember, the goal isn’t perfect organization—it’s developing deeper understanding through your notes. Let Enzyme help you turn your scattered thoughts into meaningful insights.
Have questions or need help? Reach out to us at support@enzyme.garden or join our Discord community.