Edit · Platform ← View page Saving needs a token. Register to get one. Edits are public and licensed CC-BY-SA-4.0. # The doi.bio Platform ## One Workspace for the Entire Discovery Process doi.bio eliminates context switching by bringing literature, structures, and computation into a single collaborative surface. No more toggling between PyMOL, papers, and scattered noteseverything your team needs is in one place. ## Core Capabilities ### AI-Powered Knowledge Graph Transform scattered literature into structured, queryable knowledge. **Features:** - Automatic extraction of targets, ligands, assays, and key findings from papers - Semantic linking between related concepts across publications - DOI resolution with cached, accessible content - Personal annotation and team-shared notes - Full-text search with AI-powered relevance ranking **Why It Matters:** New team members can query "What mutations confer resistance to compound X?" and get instant answers backed by the full literature context, not just paper titles. ### Interactive Molecular Context 3D structures aren't static filesthey're living, annotated knowledge objects. **Features:** - Instant access to 243K+ PDB structures and 200M+ AlphaFold predictions - Real-time collaborative viewing (see what your teammates are looking at) - Automatic pocket detection and druggability scoring - Clash detection and structure quality validation - Conservation mapping from sequence alignments - Ligand docking pose visualization - Custom annotation and measurement tools **Why It Matters:** Point to a binding pocket, and doi.bio instantly shows you all known ligands, mutations, and related structural datano manual cross-referencing needed. ### Workflow Automation with Provenance Run computations without losing track of what was tried and why. **Features:** - One-click docking, molecular dynamics, and property prediction - Visual workflow builder for multi-step analyses - Automatic capture of inputs, parameters, and results - Version control for structures and parameters - Exportable audit trails for regulatory compliance - Integration with SLURM/cloud compute **Why It Matters:** Six months later, you can see exactly why a particular compound was deprioritizedthe docking pose had a key clash that was flagged automatically. ### Team Collaboration Turn individual insights into institutional knowledge. **Features:** - Real-time multiplayer editing of notebooks and structures - @ mentions and threaded discussions - Project-based organization with granular permissions - Activity feeds showing team progress - Shareable links for external collaborators - Version history and change tracking **Why It Matters:** When your lead medicinal chemist goes on vacation, the rest of the team can see their rationale, not just their conclusions. ## Platform Architecture ### Web-First, Cloud-Native - Access from any device with a modern browser - No local software installation required - Automatic updates and backups - Elastic compute scaling for heavy workloads ### API-Driven & Extensible - RESTful API for programmatic access - Python SDK for custom scripts and notebooks - Webhook support for external tool integration - Plugin system for domain-specific extensions ### Enterprise-Ready - Single sign-on (SSO) via SAML/OAuth - Role-based access control (RBAC) - Audit logging for compliance - Data encryption in transit and at rest - On-premise deployment options ## Integration Ecosystem doi.bio works with your existing tools: ### Structural Biology - **PyMOL, ChimeraX**: Export structures with annotations intact - **Rosetta, AlphaFold**: Import predictions and run refinements - **Schrodinger, MOE**: Share ligand docking results ### Computational Chemistry - **RDKit**: Property calculations and similarity searching - **OpenEye, CCG**: Ligand-based design workflows - **Gromacs, Amber**: MD simulation setup and analysis ### Data & Notebooks - **Jupyter**: Embed doi.bio widgets in notebooks - **Spotfire, Tableau**: Export data for visualization - **ELNs (Benchling, etc.)**: Sync experimental results ### Literature & References - **Zotero, Mendeley**: Import citation libraries - **PubMed, bioRxiv**: Automated paper ingestion - **DOI APIs**: Resolve and cache full-text articles ## Security & Compliance ### Data Protection - End-to-end encryption for sensitive data - SOC 2 Type II compliance (in progress) - GDPR-compliant data handling - Regular third-party security audits ### Regulatory Support - 21 CFR Part 11 audit trails - GxP-ready workflows - Data retention policies - Export controls for sensitive research ## Performance at Scale ### Optimized for Large Datasets - Sub-second search across millions of papers - Real-time rendering of 1M+ atom structures - Parallel execution of batch computations - Intelligent caching for frequently accessed data ### Team Scalability - Supports teams from 5 to 500+ scientists - Multi-project workspaces with isolated data - Departmental and enterprise deployment models ## Pricing ### Academic **Free for Academic Research Labs** - Up to 10 users - Unlimited public projects - Community support - Access to all core features ### Startup **$499/month** - Up to 25 users - Private projects - Email support - API access - 500 compute hours/month ### Enterprise **Custom Pricing** - Unlimited users - On-premise deployment - Dedicated support - Custom integrations - SLA guarantees - Training and onboarding [Contact us for details �](/contact) ## Get Started ### Try the Live Platforms Explore doi.bio's capabilities through our demonstration surfaces: - **[c.doi.bio](https://c.doi.bio)** - Collaborative notebook - **[ci.doi.bio](https://ci.doi.bio)** - Molecular viewer - **[ai.doi.bio](https://ai.doi.bio)** - AI assistant ### Request a Demo Schedule a personalized walkthrough with our team: [Request Demo �](/contact) ### Join the Private Preview Work with us to shape the platform's development: [Apply for Early Access �](/contact) --- *doi.bio - Where papers meet proteins. 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