PapersFlow — Research MCP

Search 474M+ academic papers, verify citations, explore citation graphs, and run deep research scans — all from VS Code via the Model Context Protocol.

PapersFlow's MCP server gives GitHub Copilot Chat and any MCP-compatible AI assistant direct access to academic research tools.

Tools

Public (no account required)

Tool	Description
`search`	Full-text search across 474M+ papers
`fetch`	Fetch paper metadata by DOI, title, or URL
`verify_citation`	Normalize and verify citations
`search_literature`	Narrow literature search with filters
`find_related_papers`	Discover related work via citation graph
`get_citation_graph`	Build a full citation network
`get_paper_neighbors`	Find similar papers
`expand_citation_graph`	Recursive citation graph expansion

Authenticated (PapersFlow account required)

Tool	Description
`summarize_evidence`	Summarize DeepScan research reports
`run_deepscan`	Launch a multi-step agentic research scan
`get_deepscan_status`	Check DeepScan progress
`get_deepscan_live_snapshot`	Live progress snapshot
`get_deepscan_report`	Retrieve the full research report
`run_python_plot`	Execute Python for data visualization

Getting Started

Install this extension from the VS Code Marketplace.
Open the command palette (Ctrl+Shift+P / Cmd+Shift+P) and run PapersFlow: Show Connection Status.
Open GitHub Copilot Chat or another MCP-compatible chat surface in VS Code.
Run MCP: List Servers and confirm PapersFlow is available.
Public tools are then available immediately.
For authenticated tools, run the command palette (Ctrl+Shift+P / Cmd+Shift+P):
- PapersFlow: Set Personal Access Token
- Paste your PAT from PapersFlow Settings > Integrations.

VS Code MCP Discovery Notes

This is a normal VS Code extension that registers an MCP server definition. It is not the same thing as the @mcp gallery view in VS Code.
A fresh install may not show up in the MCP server UI until the extension activates. The most reliable first-run trigger is PapersFlow: Show Connection Status or opening chat and sending one message.
If you are checking the MCP UI immediately after install, run MCP: List Servers after activation instead of relying on the initial extension search state.

Cursor And Antigravity

Publishing to the VS Code Marketplace is enough for VS Code installs.
Cursor and Antigravity-style extension search generally rely on Open VSX-compatible distribution, not only the VS Code Marketplace listing.
If you want this extension to appear in those editors' extension search results, publish the same .vsix to Open VSX as well.

Manual MCP Config

If your editor supports direct MCP server configuration, you can connect to PapersFlow without installing this extension by pointing it at:

https://doxa.papersflow.ai/mcp

Authenticated installs should attach an Authorization: Bearer <PAT> header.

Creating a Personal Access Token

Sign in at papersflow.ai.
Go to Settings > Integrations > papersflow-mcp.
Click Create Token and select the scopes you need:
- mcp.public.read — public search and citation tools
- mcp.library.read — search your paper library
- mcp.research.read — read research reports
- mcp.research.run — run DeepScan and Python tools
Copy the token (starts with pf_pat_).

Commands

Command	Description
`PapersFlow: Set Personal Access Token`	Store your PAT securely
`PapersFlow: Clear Personal Access Token`	Remove stored PAT
`PapersFlow: Show Connection Status`	Check auth status

Settings

Setting	Default	Description
`papersflow.serverUrl`	`https://doxa.papersflow.ai/mcp`	MCP server URL

Example Prompts

Try these in GitHub Copilot Chat:

"Search for recent papers on transformer scaling laws"
"Fetch the paper with DOI 10.1038/s41586-021-03819-2 and summarize it"
"Find papers related to 'Attention Is All You Need'"
"Build a citation graph for the paper 'BERT: Pre-training of Deep Bidirectional Transformers'"
"Verify this citation: Smith et al. (2023). Deep learning in genomics. Nature Methods."

How It Works

This extension registers a PapersFlow MCP server definition with VS Code. In Cursor, it also registers the server through Cursor's MCP extension API when the host exposes that API. Once the extension is activated, an MCP-aware chat client can discover PapersFlow from the registered definition.

No local server process is launched by the extension. It connects directly to the PapersFlow hosted MCP endpoint at https://doxa.papersflow.ai/mcp, optionally attaching your PAT for authenticated tools.

PapersFlow