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How to Set Up Your Claude for Deep Research (Full Setup Guide)
Why do researchers need a second brain for Claude?
Research piles up fast. Papers, articles, interview notes, quotes, half-formed findings. Most of it ends up spread across tabs, PDFs and old chats.
Claude can help you think through all of it, but its memory only saves short summaries of your chats. The exact quote, the page number, the link to the source: those get lost.
Cleve is a second brain that plugs straight into Claude. Once it's connected, Claude has access to your entire body of research. It keeps everything organized by project, and reads from it whenever you pick the work back up.
Setup takes about 5 minutes and works on any Claude plan, including Free.
Who is this for?
Anyone whose work is mostly reading, collecting and making sense of information. For example:
Students and academics working on a thesis, paper or literature review.
Market and UX researchers collecting interviews, surveys and competitor notes.
Analysts, consultants and writers who research a topic before they write about it.
What do you need before you start?
A Claude account. Any plan works, including Free.
A Cleve account. It takes 2 minutes to create one.
Step 1: Create a Cleve account (2 mins)
Go to app.cleve.ai and sign up with Google or email. You don't need to set anything up. Claude will do that for you.
Step 2: Connect Cleve to Claude
Add Cleve as a custom connector in Claude, then sign in. It's three short steps.
1. In Claude, click + in the chat box, then Connectors, then Add custom connector.
2. Name it Cleve and paste this link: https://app.cleve.ai/mcp. Click Continue, then Add.
3. A browser tab opens. Click Continue connecting, then sign in to Cleve.
Done. Cleve is now connected to Claude.
Make sure you are signed in to the same Claude account on both your browser and the desktop app to avoid a “account mismatch” error.
Step 3: Tell Claude to run your research second brain
Paste the prompt below into your Claude chat. It tells Claude what to save, how to keep sources attached, how to organize by project, and when to look things up.
How do I know it's working?
Give Claude a source, then ask about it again in a new chat. If Claude saves it to Cleve and finds it later with the source attached, you're set.
For example, paste a link to an article or paper and ask Claude to summarize it. When it's done, Claude asks to save it to Cleve. Say yes.
Next time, just ask "what did that paper say about X?". Claude finds it in Cleve and tells you where it came from.
That's it. Cleve stores your research, Claude does the thinking, and you never lose a source again.
Ways to use it once it's set up
Literature review. Save each paper as you read it. Later, ask Claude to compare what they say on one question, with sources.
Interview and survey notes. Save each interview. Ask Claude to pull out patterns across all of them.
Running findings. Keep one findings note per project that grows as you go, so you always know where your thinking stands.
Writing it up. When it's time to write, Claude drafts from your saved notes, not from a blank page.
Frequently asked questions
Doesn't Claude already have memory?
Yes, but it saves short summaries of your chats. A second brain keeps your full notes, exact quotes and source links, so Claude can read the real thing, not a few lines about it.
Will Claude make up sources?
The prompt tells Claude to never invent a source, quote or link, and to mark anything missing as [missing]. Still, always check quotes and citations against the original before you publish or submit.
Can I save PDFs?
Claude can read a PDF you upload in the chat and save your notes, summary and key quotes from it into Cleve as a document.
Does this work on Claude's free plan?
Yes. Free plans can add one custom connector. Cleve can be that one.
How much does Cleve cost?
Cleve plans start at $8 a month (Starter), with Pro at $20 and Max at $100. Connecting to Claude works on every plan. See Cleve pricing.
I'm on a Claude Team or Enterprise plan. Why can't I add it?
On those plans, only the workspace owner can add custom connectors. Ask them to add Cleve with the link https://app.cleve.ai/mcp. Then you click Connect.
Can my research team share it?
Yes. Add teammates to your Cleve workspace and everyone's Claude can read the same notes and sources.
Will Claude delete my notes?
Not with this prompt. It tells Claude to never delete anything without asking you first.
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About the author
Lizzie · Co-founder & CMO
Lizzie is a co-founder and CMO at Cleve. She spent five years running an agency, building and managing her clients' knowledge systems on Notion. She started Cleve after watching how clients and teams struggled to build a knowledge management system they can rely on.
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