> ## Documentation Index
> Fetch the complete documentation index at: https://docs.openbio.tech/llms.txt
> Use this file to discover all available pages before exploring further.

# OpenBio User Documentation

> Welcome to OpenBio - Your AI-native platform for accelerating biological research

OpenBio is an AI-native platform designed to make cutting-edge biology accessible to every researcher. We bridge the gap between revolutionary AI models and the biologists who need them, providing a clean, focused, and intuitive user interface for complex computational tasks.

Have a look at our launch video:

<iframe className="w-full aspect-video rounded-xl" src="https://www.youtube.com/embed/sxSmazO1_hs?si=uzp7dXA6cHHXvCKw" title="YouTube video player" frameBorder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerPolicy="strict-origin-when-cross-origin" allowFullScreen />

## Getting Started

New to OpenBio? Start here to learn the basics and get up and running quickly.

<Card title="Quick Start Guide" href="/quickstart" horizontal>
  Follow our step-by-step guide to get started with OpenBio in minutes.
</Card>

## What's New

Discover the latest features and enhancements to OpenBio:

<CardGroup cols={3}>
  <Card title="OpenBio Agents" href="/user-guide/features/agents" icon="plug">
    OpenBio Special Agents are AI co-scientists designed to handle specific research workflows, providing expert guidance and automation for complex scientific tasks.
  </Card>

  <Card title="Mobile Support" href="/user-guide/features/mobile-support" icon="plug">
    Access OpenBio on the go on your mobile. Continue your research workflow from anywhere with full chat, file access, and tool execution.
  </Card>

  <Card title="Data Analysis (Code Mode)" href="/user-guide/features/data-analysis" icon="code">
    Activate Code Mode for Python-based data analysis, visualizations, and computational tasks. Execute code in a stateful Jupyter environment with pre-installed scientific libraries.
  </Card>

  <Card title="MCP Support" href="/user-guide/features/mcp-support" icon="plug">
    Extend OpenBio capabilities by connecting external MCP servers. Access documentation search, API integrations, and custom tools like Biorender, Synapse, and more.
  </Card>

  <Card title="Zotero Integration" href="/user-guide/features/zotero-support" icon="book">
    Access and manage your Zotero reference library directly from OpenBio. Search citations, organize papers, and integrate references into your research workflow.
  </Card>
</CardGroup>

### OpenBio Agents

Watch a demo of Agents in action:

<iframe className="w-full aspect-video rounded-xl" src="https://www.youtube.com/embed/2W17zRXQoCo" title="Agents Demo" frameBorder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerPolicy="strict-origin-when-cross-origin" allowFullScreen />

### Code Mode Demo

Watch Code Mode in action:

<iframe className="w-full aspect-video rounded-xl" src="https://www.youtube.com/embed/sds1Eiz0BhA" title="Code Mode Demo" frameBorder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerPolicy="strict-origin-when-cross-origin" allowFullScreen />

### Zotero Integration Demo

Watch Zotero integration in action:

<iframe className="w-full aspect-video rounded-xl" src="https://www.youtube.com/embed/J5zTULYlSBo" title="Zotero Integration Demo" frameBorder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerPolicy="strict-origin-when-cross-origin" allowFullScreen />

### MCP Integration Demo

Watch how to add BioRender MCP for template search:

<iframe className="w-full aspect-video rounded-xl" src="https://www.youtube.com/embed/gMtD0zKvY2Q" title="MCP Integration Demo - BioRender Templates" frameBorder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerPolicy="strict-origin-when-cross-origin" allowFullScreen />

## User Guide Overview

Our comprehensive user guide covers everything you need to know about using OpenBio effectively.

<CardGroup cols={2}>
  <Card title="Getting Started" href="/user-guide/getting-started/authentication">
    Learn how to create an account, sign in, and understand the OpenBio interface.
  </Card>

  <Card title="Core Features" href="/user-guide/features/chat">
    Master chat interactions, project management, file handling, and workflows.
  </Card>

  <Card title="Tools Reference" href="/user-guide/tools/overview">
    Complete reference for all available tools.
  </Card>
</CardGroup>

## What You Can Do with OpenBio

OpenBio empowers you to tackle complex biological research tasks with AI assistance:

### **Database Queries**

Search and analyze biological databases like PDB, UniProt, ChEMBL, PubMed, and AlphaFold DB using natural language.

### **Structure Prediction**

Predict protein structures from sequences using state-of-the-art AI models like BoltzGen, Boltz-2 and Chai-1.

### **Molecular Design**

Design proteins, optimize stability, create variants, and engineer new molecules.

### **Research Workflows**

Automate complex research pipelines and create reproducible protocols.

### **Data Analysis**

Use Python code execution for advanced data analysis, visualizations, and computational tasks with Code Mode.

### **Project Organization**

Manage files, notes, and research data in organized project workspaces.

### **MCP Integration**

Extend OpenBio capabilities by connecting external MCP servers for documentation search, API integrations, and custom tools like Biorender, Synapse, and more.

### **Zotero Integration**

Access and manage your Zotero reference library directly from OpenBio, search citations, and organize research papers.

### **Scientific Illustrations**

Generate publication-ready scientific figures, diagrams, and schematics using AI-powered illustration tools.

## Key Features at a Glance

### **AI-Powered Research Assistant**

* Natural language queries for complex biological tasks
* Intelligent tool selection and execution
* Real-time assistance throughout your research workflow

### **Comprehensive Tool Suite**

* Structure prediction (Boltz-2, Chai-1, SimpleFold)
* Protein design (ProteinMPNN, LigandMPNN, ThermoMPNN)
* Molecular chemistry (RDKit, SA Score)
* Database queries (PDB, UniProt, ChEMBL, PubMed, AlphaFold DB)
* And many more specialized tools

### **Advanced Analysis Capabilities**

* Side-by-side comparisons of structures and data
* Interactive 3D visualizations
* Python code execution for data analysis and visualization
* Computational workflows with stateful execution environment

### **Workflow Automation**

* Create reusable research protocols
* Automate repetitive tasks

### **Research Organization**

* Project-based workspace organization
* Integrated note-taking and todo management
* Comprehensive documentation tools
* Zotero reference library integration
* MCP server connections for extended capabilities

## Need Help?

<Card title="Frequently Asked Questions" href="/faq">
  Find answers to common questions about OpenBio.
</Card>

<Card title="Community Support" href="https://discord.gg/fd8QbDv9RQ">
  Join our community for discussions, support, and collaboration.
</Card>

<Card title="Video Tutorials" href="https://youtube.com/@openbioai?si=6hNFkgojYl0lyc6H">
  Watch video tutorials and walkthroughs on our YouTube channel.
</Card>

<Card title="Follow on Instagram" href="https://www.instagram.com/openbioai/">
  Follow us on Instagram for updates, tips, and research highlights.
</Card>