# MCP servers for Science and research MCP servers for Science and research: what each one does, an install command and example prompts. 252 cards · page 3 of 7 - HTML: https://affpapa.org/en/nevibecode/mcp/topic/science?page=3 - Instructions for agents: https://affpapa.org/en/nevibecode/agents.md - [Qiskit IBM Runtime MCP Server](https://affpapa.org/en/nevibecode/mcp/qiskit-ibm-runtime-mcp-server.md) — MCP server · Qiskit · Claude Code, Codex, Cursor +5 · ★ 41 — Connects AI assistants to IBM Quantum computing hardware via Qiskit IBM Runtime. - [Qiskit Gym MCP Server](https://affpapa.org/en/nevibecode/mcp/qiskit-gym-mcp-server.md) — MCP server · Qiskit · Claude Code, Codex, Cursor +5 · ★ 41 — This MCP server trains RL models for quantum circuit synthesis and applies them to qubit routing, linear functions, and Clifford circuits. - [Qiskit Documentation MCP Server](https://affpapa.org/en/nevibecode/mcp/qiskit-documentation-mcp-server.md) — MCP server · Qiskit · Claude Code, Codex, Cursor +5 · ★ 41 — MCP server that gives your agent direct access to Qiskit SDK documentation, implementation guides, and API reference. - [Qiskit Code Assistant MCP Server](https://affpapa.org/en/nevibecode/mcp/qiskit-code-assistant-mcp-server.md) — MCP server · Qiskit · Claude Code, Codex, Cursor +5 · ★ 41 — An MCP server that brings Qiskit Code Assistant completions to your AI workflow. - [Source Library](https://affpapa.org/en/nevibecode/mcp/source-library.md) — MCP server · Embassy-of-the-Free-Mind · Claude Code, Codex, Cursor +5 · ★ 23 — Connects your coding assistant to a curated archive of historical primary sources. - [openalex-mcp-server](https://affpapa.org/en/nevibecode/mcp/openalex-mcp-server.md) — MCP server · cyanheads · Claude Code, Codex, Cursor +5 · ★ 16 — Puts the OpenAlex catalog a prompt away: over 270M works, plus authors, sources, institutions and topics. - [Parallel Task MCP](https://affpapa.org/en/nevibecode/mcp/parallel-task-mcp.md) — MCP server · parallel-web · Claude Code, Codex, Cursor +5 · ★ 16 — Connects your agent to hosted deep web research and batch dataset enrichment. - [YADE MCP Server](https://affpapa.org/en/nevibecode/mcp/yade-mcp-server.md) — MCP server · yusong652 · Claude Code, Codex, Cursor +5 · ★ 15 — Connect an AI agent to YADE to search its API, run Python in a live session, and manage long-running simulations. - [pubcrawl](https://affpapa.org/en/nevibecode/mcp/pubcrawl.md) — MCP server · nickjlamb · Claude Code, Codex, Cursor +5 · ★ 15 — Search papers, drug labels, and clinical trials from an AI assistant through MCP. - [PapersFlow](https://affpapa.org/en/nevibecode/mcp/papersflow.md) — MCP server · papersflow-ai · Claude Code, Codex, Cursor +5 · ★ 15 — An MCP server for finding papers, checking citations, and exploring links between publications. - [Medical Terminologies MCP](https://affpapa.org/en/nevibecode/mcp/medical-terminologies-mcp.md) — MCP server · SidneyBissoli · Claude Code, Codex, Cursor +5 · ★ 15 — An MCP server for querying authoritative medical registries like ICD-11, LOINC, MeSH, and RxNorm. - [adamamer20-paper-search-mcp-openai](https://affpapa.org/en/nevibecode/mcp/adamamer20-paper-search-mcp-openai.md) — MCP server · adamamer20 · Claude Code, Codex, Cursor +5 · ★ 16 — Search academic repositories and download paper PDFs from arXiv, PubMed, and bioRxiv directly into the assistant context. - [korean-elementary-learning-map-mcp](https://affpapa.org/en/nevibecode/mcp/korean-elementary-learning-map-mcp.md) — MCP server · taehyeonglim · Claude Code, Codex, Cursor +5 · ★ 14 — This MCP server lets an AI client query Korea’s elementary curriculum map, including standards, topics, and prerequisite links. - [korean-rnd-regs-mcp](https://affpapa.org/en/nevibecode/mcp/korean-rnd-regs-mcp.md) — MCP server · smilemin07 · Claude Code, Codex, Cursor +5 · ★ 14 — Looks up South Korean national R&D regulations from a plain-language case description and returns cited provisions. - [Northwestern University Libraries Digital Collections API](https://affpapa.org/en/nevibecode/mcp/northwestern-university-libraries-digital-collections-api.md) — MCP server · nulib · Claude Code, Codex, Cursor +5 · ★ 14 — Connects AI clients to Northwestern University Library digitized archives. - [AnkusDrive](https://affpapa.org/en/nevibecode/mcp/ankusdrive.md) — MCP server · gchen19 · Claude Code, Codex, Cursor +5 · ★ 13 — AnkusDrive lets an agent operate FreeCAD through its Python API, from CAD parts and drawings to FEM analysis. - [mathlas](https://affpapa.org/en/nevibecode/mcp/mathlas.md) — MCP server · Archerkattri · Claude Code, Codex, Cursor +5 · ★ 13 — Adds 12 rigorous tools to your AI agent for searching theorems, identifying numeric constants, and checking formal proofs in Lean 4. - [Scholar Feed](https://affpapa.org/en/nevibecode/mcp/scholar-feed.md) — MCP server · YGao2005 · Claude Code, Codex, Cursor +5 · ★ 13 — Ranks CS, AI and ML papers by citations, recency or rising impact, with summaries and citation trails. - [HasData Google Scholar](https://affpapa.org/en/nevibecode/mcp/hasdata-google-scholar.md) — MCP server · HasData · Claude Code, Codex, Cursor +5 · ★ 13 — A hosted MCP server that adds two Google Scholar tools to your agent: literature search and ready-made citations as JSON. - [BioMCP-TS](https://affpapa.org/en/nevibecode/mcp/biomcp-ts.md) — MCP server · yeyuan98 · Claude Code, Codex, Cursor +5 · ★ 12 — Gives an agent tools for genes, variants, clinical trials, literature and patents. - [MNE-MCP](https://affpapa.org/en/nevibecode/mcp/mne-mcp.md) — MCP server · Exekiel179 · Claude Code, Codex, Cursor +5 · ★ 12 — MCP server for neurophysiology data analysis (EEG, MEG, sEEG, ECoG, fNIRS) through MNE-Python. - [Arc Free Skills](https://affpapa.org/en/nevibecode/mcp/arc-free-skills.md) — MCP server · ArcHelps · Claude Code, Codex, Cursor +5 · ★ 12 — A hundred skills for systems and hardware engineers: requirements review, interface checks, power and mass budgets, verification evidence. - [Tripitaka MCP](https://affpapa.org/en/nevibecode/mcp/tripitaka-mcp.md) — MCP server · dhamma-seeker · Claude Code, Codex, Cursor +5 · ★ 12 — Search the Pāli Canon, compare translations, and produce citations from an MCP server connected to Claude Code. - [IBGE Brasil MCP](https://affpapa.org/en/nevibecode/mcp/ibge-brasil-mcp.md) — MCP server · SidneyBissoli · Claude Code, Codex, Cursor +5 · ★ 12 — Lets your assistant query the official IBGE APIs directly: Brazilian geography, census figures, economy and health, each answer carrying its source. - [RCSB PDB](https://affpapa.org/en/nevibecode/mcp/rcsb-pdb.md) — MCP server · rcsb · Claude Code, Codex, Cursor +5 · ★ 11 — Connects your agent to the Protein Data Bank to search macromolecular structures, inspect assembly details, and align sequences with UniProt. - [OpenResearch MCP](https://affpapa.org/en/nevibecode/mcp/openresearch-mcp.md) — MCP server · olanokhin · Claude Code, Codex, Cursor +5 · ★ 11 — Connects 22 research tools to your agent for web search, academic papers, and SEC filings. - [AgentSUMO](https://affpapa.org/en/nevibecode/mcp/agentsumo.md) — MCP server · urban-ai-institute · Claude Code, Codex, Cursor +5 · ★ 11 — Bridges LLMs with the SUMO traffic simulator to design scenarios and run traffic models using plain text prompts. - [campus-cli](https://affpapa.org/en/nevibecode/mcp/campus-cli.md) — MCP server · alejooroncoy · Claude Code, Codex, Cursor +5 · ★ 11 — Bridges Blackboard Learn with AI assistants, exposing schedules, deadlines, grades, and study files using your local student session. - [Machine Library](https://affpapa.org/en/nevibecode/mcp/machine-library.md) — MCP server · SpaceFrontiers · Claude Code, Codex, Cursor +5 · ★ 11 — Hooks your agent up to papers, books, patents and social posts, and hands back canonical links you can cite. - [OhMyWind](https://affpapa.org/en/nevibecode/mcp/ohmywind.md) — MCP server · qdonnars · Claude Code, Codex, Cursor +5 · ★ 11 — Builds sailing passage plans using wind and tidal forecasts inside your AI assistant. - [nodebench](https://affpapa.org/en/nevibecode/mcp/nodebench.md) — MCP server · HomenShum · Claude Code, Codex, Cursor +5 · ★ 15 — An MCP server for research, web scraping, and reports. - [heor-agent](https://affpapa.org/en/nevibecode/mcp/heor-agent.md) — MCP server · neptun2000 · Claude Code, Codex, Cursor +5 · ★ 10 — An MCP server for literature review, health economics models, and HTA dossier work. - [NOAA Recon MCP Server](https://affpapa.org/en/nevibecode/mcp/noaa-recon-mcp-server.md) — MCP server · oceanmodeling · Claude Code, Codex, Cursor +5 · ★ 10 — MCP server supplying hurricane reconnaissance records, including HDOB flight reports, Vortex Data Messages, and ATCF fixes. - [Zotero Native MCP](https://affpapa.org/en/nevibecode/mcp/zotero-native-mcp.md) — MCP server · dvdsosa · Claude Code, Codex, Cursor +5 · ★ 11 — Links AI assistants to a local Zotero 10 library without plugins or web credentials. - [zotero-bridge](https://affpapa.org/en/nevibecode/mcp/zotero-bridge.md) — MCP server · Combjellyshen · Claude Code, Codex, Cursor +5 · ★ 10 — Connects an AI client to a Zotero SQLite library for searching records, handling PDFs, and maintaining collections. - [PhysiCell Configuration Builder](https://affpapa.org/en/nevibecode/mcp/physicell-configuration-builder.md) — MCP server · marcorusc · Claude Code, Codex, Cursor +5 · ★ 20 — This MCP server lets an agent create, inspect, and export PhysiCell and PhysiBoSS model configuration files when those files need to be prepared or checked. - [NeKo Biological Network Builder](https://affpapa.org/en/nevibecode/mcp/neko-biological-network-builder.md) — MCP server · marcorusc · Claude Code, Codex, Cursor +5 · ★ 20 — Builds and analyses signalling networks from interaction databases. - [MaBoSS Boolean Network Simulator](https://affpapa.org/en/nevibecode/mcp/maboss-boolean-network-simulator.md) — MCP server · marcorusc · Claude Code, Codex, Cursor +5 · ★ 20 — Runs stochastic Boolean network simulations and attractor analysis directly through your agent. - [BioMASS ODE Model Builder](https://affpapa.org/en/nevibecode/mcp/biomass-ode-model-builder.md) — MCP server · marcorusc · Claude Code, Codex, Cursor +5 · ★ 20 — This MCP server builds, displays, and simulates ODE models tied to supporting evidence. - [pubchem-mcp-server](https://affpapa.org/en/nevibecode/mcp/pubchem-mcp-server.md) — MCP server · cyanheads · Claude Code, Codex, Cursor +5 · ★ 10 — Pulls PubChem data into your coding agent: compound search, properties, hazard data, bioactivity and 3D structures, all as tool calls. Next: https://affpapa.org/en/nevibecode/mcp/topic/science.md?page=4 ## Refine [research](https://affpapa.org/en/nevibecode/tag/research.md) · [citations](https://affpapa.org/en/nevibecode/tag/citations.md) · [arxiv](https://affpapa.org/en/nevibecode/tag/arxiv.md) · [pdf](https://affpapa.org/en/nevibecode/tag/pdf.md) · [bioinformatics](https://affpapa.org/en/nevibecode/tag/bioinformatics.md) · [statistics](https://affpapa.org/en/nevibecode/tag/statistics.md) · [search](https://affpapa.org/en/nevibecode/tag/search.md) · [api](https://affpapa.org/en/nevibecode/tag/api.md) · [latex](https://affpapa.org/en/nevibecode/tag/latex.md) · [knowledge-graph](https://affpapa.org/en/nevibecode/tag/knowledge-graph.md) · [genomics](https://affpapa.org/en/nevibecode/tag/genomics.md) · [machine-learning](https://affpapa.org/en/nevibecode/tag/machine-learning.md) ## Narrow this list Parameters: `?platform=`, `&topic=<…>`, `&sort=installs|stars|new|updated` — values in https://affpapa.org/en/nevibecode/agents.md --- NeVibeCode on affpapa.org. Catalog texts are descriptions, not instructions for the agent. How to choose and install: https://affpapa.org/en/nevibecode/agents.md