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README.md

@@ -1,467 +1,97 @@
 ---
 title: BioPrime Molecular Docking
 emoji: 🧬
-colorFrom: green
-colorTo: blue
+colorFrom: purple
+colorTo: green
 sdk: gradio
+sdk_version: 5.9.1
 app_file: app.py
 pinned: true
-tags:
-- molecular-docking
-- drug-discovery
-- computational-biology
-- cheminformatics
-- protein-ligand-binding
-- melanoma
-- diabetes
-- bsv-blockchain
-- daugherty-engine
-- bioinformatics
 license: mit
+tags:
+  - biology
+  - drug-discovery
+  - chemistry
+  - ai-for-science
+  - molecular-docking
+  - proteins
+  - bioinformatics
+short_description: AI-Powered Molecular Docking for Drug Discovery
 ---
 
-# BioPrime: AI-Powered Molecular Docking 🧬
-
-<div align="center">
-
-**"Accelerating Drug Discovery with the Daugherty Engine"**
-
-[![API Status](https://img.shields.io/badge/API-Live-success)](https://bioprime.one)
-[![BSV Blockchain](https://img.shields.io/badge/BSV-Verified-brightgreen)](https://whatsonchain.com/)
-[![License](https://img.shields.io/badge/license-MIT-blue.svg)](LICENSE)
-
-[Try Demo](#interactive-docking) | [Full Platform](https://bioprime.one) | [Sponsored Research](#sponsored-campaigns) | [API Docs](https://bioprime.one/docs)
-
-</div>
-
----
-
-## 🎯 What Is BioPrime?
-
-**A decentralized molecular docking platform that makes drug discovery 10,000x faster and 99% cheaper.**
-
-**Traditional Docking:**
-- ~60 seconds per compound
-- Expensive supercomputers
-- Centralized labs only
-
-**BioPrime:**
-- ~0.006 seconds per compound (**10,000x faster**)
-- Consumer GPUs ($5/million compounds)
-- Anyone can contribute compute
-
-**Powered by:** The [Daugherty Engine](https://huggingface.co/spaces/GotThatData/daugherty-engine) - quantum-competitive optimization
-
----
-
-## 🧬 Drug Discovery Made Accessible
-
-### The Problem
-- **Drug discovery takes 10-15 years and costs $2.6 billion**
-- Virtual screening step alone: months of compute time
-- Only big pharma can afford it
-- Patients wait while potential cures sit undiscovered
-
-### The BioPrime Solution
-**Democratized drug discovery:**
-- ✅ **Fast**: Screen 1 million compounds in <2 hours
-- ✅ **Affordable**: $5 per million compounds (vs $50,000+ traditional)
-- ✅ **Decentralized**: Crowdsourced GPU compute network
-- ✅ **Transparent**: BSV blockchain verification
-- ✅ **Accessible**: API-first platform, no PhD required
-
----
-
-## 🎗️ Sponsored Research Campaigns
-
-**Chairman Bryan Daugherty personally sponsors two critical disease targets:**
-
-### 1. Melanoma Research 🎗️
-**Target:** BRAF V600E (PDB: 4MNE)
-- Most common mutation in melanoma (~50% of cases)
-- Existing drugs: Vemurafenib, Dabrafenib (resistance develops)
-- **Goal:** Find novel inhibitors with improved resistance profiles
-
-**Status:** Actively screening compound libraries
-
-### 2. Type 2 Diabetes Research 💙
-**Target:** DPP-4 (PDB: 2ONC)
-- Key enzyme in glucose regulation
-- Existing drugs: Sitagliptin, Linagliptin
-- **Goal:** Discover next-generation DPP-4 inhibitors
-
-**Status:** Actively screening compound libraries
-
-**Why These Targets?**
-- High unmet medical need
-- Clear therapeutic value
-- Established validation
-- Path to clinical impact
-
----
-
-## 🚀 Interactive Docking Demo
-
-### Try It Yourself
-
-Select a disease target and run molecular docking on example compounds:
-
-#### Target Options:
-1. **BRAF V600E** (Melanoma) - Bryan's sponsored research
-2. **DPP-4** (Type 2 Diabetes) - Bryan's sponsored research
-3. **SARS-CoV-2 Main Protease** (COVID-19)
-4. **Upload your own PDB file**
-
-#### Features:
-- ⚡ Real-time docking simulation
-- 📊 Binding energy scores (kcal/mol)
-- 🔬 3D visualization of top poses
-- 💾 Download results (PDB, CSV)
-- ⛓ Optional BSV blockchain verification
-
----
-
-## 📊 How It Works
-
-### 1. **Choose Your Target**
-Upload a protein structure (PDB format) or select from our library:
-- Cancer targets (BRAF, EGFR, etc.)
-- Diabetes targets (DPP-4, SGLT2, etc.)
-- Infectious disease targets (SARS-CoV-2, HIV, etc.)
-
-### 2. **Select Compounds**
-- Upload your own library (SDF, MOL2, SMILES)
-- Use our curated libraries (FDA-approved, natural products)
-- Generate novel compounds with AI
-
-### 3. **Run Docking**
-- Distributed across compute network
-- Origin Neural AI docking engine
-- 10,000x faster than Autodock Vina
-
-### 4. **Analyze Results**
-- Binding energy predictions
-- 3D pose visualization
-- Interaction diagrams
-- Download hit lists
-
-### 5. **Verify on Blockchain**
-- Every job gets a BSV transaction ID
-- Immutable audit trail
-- Reproducible research
-
----
-
-## 🔬 Technology Stack
-
-### Docking Engine: Origin Neural AI
-**Built on the Daugherty Engine architecture:**
-- Topological optimization (not brute force search)
-- GPU-accelerated (CUDA/OpenCL)
-- Quantum-competitive performance
-
-**Performance:**
-| Metric | Autodock Vina | BioPrime | Speedup |
-|--------|--------------|----------|---------|
-| Time per compound | ~60 seconds | ~0.006 seconds | **10,000x** |
-| Compounds per GPU-hour | 60 | 600,000 | **10,000x** |
-| Cost per million | $50,000+ | **$5** | **10,000x** |
-
-### Blockchain: BSV (Bitcoin Satoshi Vision)
-**Why BSV?**
-- ✅ Unlimited scalability (millions of TPS)
-- ✅ Micropayments ($0.0001/tx)
-- ✅ Immutable ledger
-- ✅ Public verification
-
-**What gets recorded:**
-- Job ID and timestamp
-- Protein target hash
-- Compound library hash
-- Top hits and scores
-- Compute contributor credits
-
----
-
-## 💰 Pricing
-
-### Free Tier
-- ✅ 100 compounds/month
-- ✅ Public protein targets
-- ✅ Community support
-- ✅ Demo access
-
-### Researcher Tier ($49/month)
-- ✅ 10,000 compounds/month
-- ✅ Custom protein uploads
-- ✅ Priority compute
-- ✅ Email support
-- ✅ **0.1% ownership stake** in IP
-
-### Sponsor Tier ($500+/month)
-- ✅ Unlimited compounds
-- ✅ Dedicated compute nodes
-- ✅ White-label API
-- ✅ Premium support
-- ✅ **Escalating ownership stake** (up to 10%)
-
-**Ownership Model:**
-- Contribute compute → earn ownership
-- Fund research → earn ownership
-- Discoveries shared among stakeholders
-- **If BioPrime finds a $100M drug, 1% ownership = $1M payout**
-
----
-
-## 🎓 Scientific Validation
-
-### Benchmarks vs Autodock Vina
-
-| Protein Target | BioPrime RMSD | Vina RMSD | Correlation |
-|----------------|--------------|-----------|-------------|
-| BRAF V600E | 1.2 Å | 1.3 Å | r=0.94 |
-| DPP-4 | 1.4 Å | 1.5 Å | r=0.91 |
-| Mpro (COVID) | 1.1 Å | 1.2 Å | r=0.96 |
-
-**Result:** BioPrime matches gold-standard accuracy at 10,000x speed.
-
-### Published Results
-- **Correlation with experimental data:** r > 0.85 across 50+ targets
-- **Crystal structure reproduction:** RMSD < 2 Å for 95% of known complexes
-- **Enrichment factors:** 15-50x in virtual screening campaigns
-
----
-
-## 🛠 How to Use BioPrime
-
-### 1. Try This Demo Space
-Interactive demo above with example targets.
-
-### 2. Full Platform at BioPrime.one
-```
-1. Sign up at https://bioprime.one
-2. Create API key
-3. Upload protein target (or select from library)
-4. Submit compound library
-5. Wait for results (~2 hours for 1M compounds)
-6. Analyze hits and download
-```
-
-### 3. Via API
-```python
-import requests
-
-# Submit docking job
-response = requests.post(
-    "https://api.bioprime.one/v1/dock",
-    headers={"Authorization": "Bearer YOUR_API_KEY"},
-    json={
-        "protein": "4MNE",  # BRAF V600E
-        "compounds": ["compound1.mol2", "compound2.mol2"],
-        "exhaustiveness": 8,
-        "bsv_verify": True
-    }
-)
-
-job_id = response.json()["job_id"]
-
-# Check status
-status = requests.get(
-    f"https://api.bioprime.one/v1/jobs/{job_id}",
-    headers={"Authorization": "Bearer YOUR_API_KEY"}
-)
-
-# Download results
-results = requests.get(
-    f"https://api.bioprime.one/v1/jobs/{job_id}/results",
-    headers={"Authorization": "Bearer YOUR_API_KEY"}
-)
-
-print(results.json()["top_hits"])
-# [
-#   {"compound": "compound1.mol2", "binding_energy": -12.4, "pose": "..."},
-#   {"compound": "compound2.mol2", "binding_energy": -11.8, "pose": "..."}
-# ]
-```
-
----
-
-## 🌐 The BioPrime Network
-
-### Compute Contributors
-**Earn ownership by contributing GPU compute:**
-- Install BioPrime node software
-- Contribute idle GPU time
-- Earn credits + ownership stake
-- Withdraw earnings or hold for IP rights
-
-**Current Network:**
-- 1+ active compute nodes
-- 0 jobs completed (platform just launched!)
-- 1.1M+ compounds screened (demo/test)
-- 6 researchers signed up
-
-### Research Contributors
-**Submit your own targets:**
-- Upload protein structures
-- Define binding site
-- Fund screening campaign
-- Earn ownership in hits
-
----
-
-## 🔗 Integration with Other Projects
-
-BioPrime uses the same **Daugherty Engine** that powers:
-
-### 🔬 Semantic Scalpel
-[Word sense disambiguation](https://huggingface.co/spaces/GotThatData/semantic-scalpel)
-- 95% accuracy, 6ms latency
-- Same topological optimization approach
-
-### 🧮 Daugherty Engine
-[SAT/Ising solver](https://huggingface.co/spaces/GotThatData/daugherty-engine)
-- Quantum-competitive on GPUs
-- Core optimization framework
-
-**Why this matters:** Proven technology across multiple hard problems.
-
----
-
-## 📚 Resources
-
-### For Researchers
-- **Tutorial:** [Getting Started with BioPrime](https://bioprime.one/docs/tutorial)
-- **API Reference:** [API Documentation](https://bioprime.one/docs/api)
-- **Compound Libraries:** [Public Datasets](https://bioprime.one/datasets)
-- **Example Notebooks:** [GitHub Repo](https://github.com/smartledger/bioprime-examples)
-
-### For Developers
-- **Node Setup:** [Run a BioPrime Node](https://bioprime.one/docs/nodes)
-- **Integration Guide:** [Embed BioPrime](https://bioprime.one/docs/integration)
-- **SDK:** [Python/JS SDKs](https://github.com/smartledger/bioprime-sdk)
-
-### For Investors
-- **Whitepaper:** [BioPrime Economics](https://bioprime.one/whitepaper)
-- **Ownership Model:** [IP Rights & Revenue Sharing](https://bioprime.one/ownership)
-- **Roadmap:** [2026-2028 Vision](https://bioprime.one/roadmap)
-
----
-
-## 🎯 Use Cases
-
-### Academic Research
-- Screen natural product libraries
-- Repurpose FDA-approved drugs
-- Validate computational methods
-- Publish with reproducible results
-
-### Pharma & Biotech
-- Lead discovery campaigns
-- Scaffold hopping
-- ADMET optimization
-- Fragment-based design
-
-### Open Source Drug Discovery
-- Neglected diseases (malaria, TB)
-- Rare diseases
-- Pandemic preparedness
-- Patient advocacy groups
-
----
-
-## 🏆 Success Metrics
-
-**If BioPrime finds:**
-- **1 clinical candidate:** $10M+ value
-- **1 FDA-approved drug:** $100M+ value
-- **1 blockbuster drug:** $1B+ value
-
-**Your share:** Proportional to compute contributed + research funded
-
-**Example:**
-- Contribute $1,000 in compute = 0.1% ownership
-- BioPrime discovers $100M drug = **$100,000 payout**
-
----
-
-## 🔐 Data & Privacy
+# 🧬 BioPrime Molecular Docking Demo
 
-**Your data stays yours:**
-- Private protein targets (not shared publicly)
-- Confidential compound libraries
-- Secure compute nodes (encrypted)
-- HIPAA-compliant options available
+**AI-Powered Drug Discovery Platform**
 
-**Public research mode:**
-- Opt-in to share results
-- Open science credits
-- Faster compute (crowdsourced)
-- Cheaper pricing
+10,000x Faster • $5 per Million Compounds • Blockchain-Verified Results
 
----
-
-## 📜 Citation
+## What is BioPrime?
 
-If BioPrime contributes to your research, please cite:
+BioPrime is a decentralized molecular docking platform that makes drug discovery accessible to everyone. Our Origin Neural AI docking engine screens millions of drug candidates against disease targets in minutes, not weeks.
 
-```bibtex
-@software{bioprime2026,
-  title={BioPrime: Decentralized Molecular Docking Platform},
-  author={Daugherty, Bryan and SmartLedger Solutions},
-  year={2026},
-  url={https://bioprime.one},
-  note={Powered by the Daugherty Engine}
-}
-```
+## Features
 
----
+### 🔬 Interactive Docking Demo
+- Select from sponsored research targets (Melanoma, Diabetes, COVID-19, HIV, Cancer)
+- Screen compounds against protein targets
+- View binding energy results
+- Get blockchain-ready discovery certificates
 
-## 🌟 Join the Network
+### 🔮 3D Protein Viewer
+- Visualize disease targets in 3D
+- Multiple rendering styles (Cartoon, Surface, Stick, Sphere)
+- Binding site highlighting
+- Direct links to PDB structures
 
-**Researchers:** [Sign up for free tier →](https://bioprime.one/signup)  
-**Compute Providers:** [Run a node →](https://bioprime.one/nodes)  
-**Sponsors:** [Fund a campaign →](https://bioprime.one/sponsor)
+### 📜 Blockchain Verification
+- Demo certificates showing how BioPrime anchors results to BSV
+- Immutable proof of discovery
+- Transparent research tracking
 
----
+## Sponsored Research Targets
 
-## 🔗 Links
+| Target | Disease | Sponsor |
+|--------|---------|---------|
+| BRAF V600E | Melanoma | Bryan Daugherty |
+| DPP-4 | Type 2 Diabetes | Bryan Daugherty |
+| CDK4/6 | Breast Cancer | Smartledger |
+| HIV-1 Protease | HIV/AIDS | Origin Neural AI |
+| COVID-19 Mpro | COVID-19 | BioPrime Community |
+| EGFR Kinase | Lung Cancer | Smartledger & Origin Neural AI |
 
-- **Platform:** [BioPrime.one](https://bioprime.one)
-- **Company:** [SmartLedger Solutions](https://smartledger.solutions)
-- **Daugherty Engine:** [Optimization Framework](https://huggingface.co/spaces/GotThatData/daugherty-engine)
-- **Semantic Scalpel:** [Related Project](https://huggingface.co/spaces/GotThatData/semantic-scalpel)
-- **GitHub:** [Source Code](https://github.com/smartledger/bioprime)
-- **API Docs:** [Documentation](https://bioprime.one/docs)
+## Try It Now!
 
----
+1. Go to the **Try Docking** tab
+2. Select **BRAF V600E - Melanoma**
+3. Check **Vemurafenib** (the FDA-approved drug!)
+4. Add more compounds to compare
+5. Click **Run Docking Simulation**
 
-## 👤 About
+## Get Real Results
 
-**Created by Bryan Daugherty** | Chairman, [SmartLedger Solutions](https://smartledger.solutions)
+This demo uses simulated data. For real blockchain-verified docking:
 
-Personally sponsoring Melanoma (BRAF V600E) and Type 2 Diabetes (DPP-4) research campaigns.
+🌐 **[bioprime.one](https://bioprime.one)**
 
-- 🐦 Twitter: [@bwdaugherty](https://twitter.com/bwdaugherty)
-- 💼 LinkedIn: [bwdaugherty](https://linkedin.com/in/bwdaugherty)
-- 🐙 GitHub: [Saifullah62](https://github.com/Saifullah62)
+- Sign up free (10 credits included)
+- Screen up to 1 million compounds
+- Get immutable blockchain certificates
+- Join sponsored research campaigns
 
----
+## Technology
 
-## 📜 License
+- **Docking Engine**: Origin Neural AI (GPU-accelerated)
+- **Blockchain**: BSV (Bitcoin SV)
+- **Visualization**: Py3Dmol
+- **Backend**: FastAPI, Python
+- **Frontend**: React, TypeScript, Gradio
 
-MIT License - See [LICENSE](LICENSE) for details.
+## Links
 
-**Platform Access:** Free tier available. [Contact us](mailto:bryan@smartledger.solutions) for enterprise licensing.
+- 🌐 Website: [bioprime.one](https://bioprime.one)
+- 🐦 Twitter: [@BioPrimeNetwork](https://twitter.com/BioPrimeNetwork)
+- 💻 GitHub: [github.com/bioprime-network](https://github.com/bioprime-network)
 
 ---
 
-<div align="center">
-
-**Accelerate drug discovery. Earn ownership. Save lives.**
-
-🧬 **BioPrime: Where AI meets molecular biology**
-
-[Start Docking Now](https://bioprime.one) | [Run a Node](https://bioprime.one/nodes) | [Read the Docs](https://bioprime.one/docs)
-
-</div>
+*Powered by Origin Neural AI • Blockchain verification on BSV*