paper-search-mcp MCP — Use Cases, Install & Live Demo

Why use it

Key features

Unified search_papers across 20+ sources
Platform-specific search + download tools per source
download_with_fallback picks the best source for a DOI
Free-first: public sources by default, paid optional
Python + uvx install

Live Demo

What it looks like in practice

paper-search.replay ▶ ready

0/0

Install

Pick your client

~/Library/Application Support/Claude/claude_desktop_config.json · Windows: %APPDATA%\Claude\claude_desktop_config.json

{
  "mcpServers": {
    "paper-search": {
      "command": "uvx",
      "args": [
        "paper-search-mcp"
      ],
      "_inferred": true
    }
  }
}

Open Claude Desktop → Settings → Developer → Edit Config. Restart after saving.

~/.cursor/mcp.json · .cursor/mcp.json

{
  "mcpServers": {
    "paper-search": {
      "command": "uvx",
      "args": [
        "paper-search-mcp"
      ],
      "_inferred": true
    }
  }
}

Cursor uses the same mcpServers schema as Claude Desktop. Project config wins over global.

VS Code → Cline → MCP Servers → Edit

{
  "mcpServers": {
    "paper-search": {
      "command": "uvx",
      "args": [
        "paper-search-mcp"
      ],
      "_inferred": true
    }
  }
}

Click the MCP Servers icon in the Cline sidebar, then "Edit Configuration".

~/.codeium/windsurf/mcp_config.json

{
  "mcpServers": {
    "paper-search": {
      "command": "uvx",
      "args": [
        "paper-search-mcp"
      ],
      "_inferred": true
    }
  }
}

Same shape as Claude Desktop. Restart Windsurf to pick up changes.

~/.continue/config.json

{
  "mcpServers": [
    {
      "name": "paper-search",
      "command": "uvx",
      "args": [
        "paper-search-mcp"
      ]
    }
  ]
}

Continue uses an array of server objects rather than a map.

~/.config/zed/settings.json

{
  "context_servers": {
    "paper-search": {
      "command": {
        "path": "uvx",
        "args": [
          "paper-search-mcp"
        ]
      }
    }
  }
}

Add to context_servers. Zed hot-reloads on save.

claude mcp add paper-search -- uvx paper-search-mcp

One-liner. Verify with claude mcp list. Remove with claude mcp remove.

Use Cases

Real-world ways to use paper-search-mcp

How to build a literature review bibliography from a prompt

👤 Researchers, grad students ⏱ ~30 min intermediate

When to use: New topic, need a starting set of 20-50 papers.

Prerequisites

uv — brew install uv

Flow

Broad search

search_papers 'mechanistic interpretability attention heads' across arXiv, Semantic Scholar, OpenAlex. Return top 30 by citations.✓ Copied

→ Cross-source list with titles, authors, citation counts
Download the winners

For the top 10 by citation, download_with_fallback to /papers/interp/.✓ Copied

→ PDFs saved
Extract abstracts

Read each PDF's abstract and produce a grouped summary.✓ Copied

→ Grouped bibliography

Outcome: Starter bibliography you can actually read.

Pitfalls

Duplicate entries across sources — Deduplicate by DOI before ranking
Closed-access papers without OA versions — Use download_with_fallback which tries OA mirrors (arXiv, Unpaywall) first

Combine with: filesystem

How to find the latest papers on a topic since a date

👤 Researchers tracking a fast-moving area ⏱ ~20 min beginner

When to use: Weekly/monthly scan.

Flow

Date-bounded search

search_arxiv 'constitutional AI' submitted after 2026-01-01. Sort by date desc.✓ Copied

→ Recent list
Read new abstracts

For each new paper, get the abstract and tag: confirms prior work / extends / contradicts / unrelated.✓ Copied

→ Tagged triage

Outcome: Up-to-date view without wading through the whole feed.

Combine with: notion

How to cross-check a clinical claim in PubMed + Europe PMC

👤 Clinicians, biotech researchers ⏱ ~25 min intermediate

When to use: A patient-facing doc makes a claim and you want to verify.

Flow

Search PubMed

search_pubmed 'metformin cognitive decline' — RCTs only, 2020+.✓ Copied

→ RCT list
Pull full context from Europe PMC if needed

For the top 5, check if Europe PMC has the full text (OA).✓ Copied

→ Full texts where available

Outcome: Source-backed verification.

Pitfalls

Do not rely on abstracts alone for clinical decisions — Read the actual methodology before citing

Combinations

Pair with other MCPs for X10 leverage

paper-search + markdownify

Convert downloaded PDFs to markdown for RAG ingestion

For every PDF in /papers/interp/, run pdf-to-markdown and save to /kb/papers/.✓ Copied

paper-search + deep-research

Cross-check a deep research report's sources against arXiv

Given this deep research report, identify any 2024-2026 arXiv papers missing from the citations.✓ Copied

paper-search + notion

Maintain a research reading log

Add each newly-downloaded paper to the Notion 'Reading Log' database with title, authors, DOI, and a 3-line summary.✓ Copied

Tools

What this MCP exposes

Tool	Inputs	When to call	Cost
search_papers	query, sources?: str[], limit?: int, year_min?: int	Multi-source search	free (public APIs)
download_with_fallback	doi_or_arxiv_id, dest_dir	Get PDF via best available route	free
search_arxiv	query, sort?, year_min?	arXiv-specific	free
download_arxiv	arxiv_id, dest_dir	Get arXiv PDF	free
search_pubmed	query, filters?	Biomedical search	free
search_semantic_scholar	query	Citation-aware search	free
search_biorxiv	query	Biology preprints	free

Cost & Limits

What this costs to run

API quota: Public APIs have per-IP rate limits (arXiv 3 req/s, PubMed 3/s without key)
Tokens per call: Search metadata: 200-1000 tokens per paper; PDFs are file-based (no token cost)
Monetary: Free for public sources; paid sources (IEEE, ACM) need their own keys
Tip: Get a free NCBI API key for 10x PubMed rate; arXiv has no key but respect the 3 req/s limit.

Security

Permissions, secrets, blast radius

Minimum scopes: Filesystem write to your download directory Optional keys for paid sources

Credential storage: Env vars for optional API keys

Data egress: Hits the public academic APIs you enable

Never grant: Nothing destructive — all read/download

Respect per-source terms of use — bulk downloading can get your IP blocked.

Troubleshooting

Common errors and fixes

429 rate limit

Throttle — arXiv needs 3 req/s max, PubMed without key is 3/s. Back off.

download_with_fallback fails for a closed-access DOI

No legal free source exists. Use your library's subscription; this tool only uses OA routes.

Search returns fewer results than the source's website

Some APIs have narrower indexes than their UIs. Cross-check with search_semantic_scholar which has broad coverage.

PDF downloaded but unreadable

Source may return an HTML splash page instead of PDF; check file type and report via the issue tracker.

Verify: file path/to/downloaded.pdf

Alternatives

paper-search-mcp vs others

Alternative	When to use it instead	Tradeoff
arxiv-mcp	You only need arXiv, nothing else	Single-source only
deep-research MCP	You want synthesis, not just retrieval	LLM costs; different shape

More

Resources

📖 Read the official README on GitHub

🐙 Browse open issues

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