zax.doi.bio/platform
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
Get Started
Try the Live Platforms
Explore doi.bio's capabilities through our demonstration surfaces:
- c.doi.bio - Collaborative notebook
- ci.doi.bio - Molecular viewer
- ai.doi.bio - AI assistant
Request a Demo
Schedule a personalized walkthrough with our team:
Join the Private Preview
Work with us to shape the platform's development:
doi.bio - Where papers meet proteins. Where teams move faster.