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app.py
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| 1 |
+
"""
|
| 2 |
+
BioPrime Molecular Docking Demo
|
| 3 |
+
================================
|
| 4 |
+
Interactive demo showcasing AI-powered molecular docking for drug discovery.
|
| 5 |
+
|
| 6 |
+
Features:
|
| 7 |
+
- 3D protein structure visualization
|
| 8 |
+
- Compound library selection
|
| 9 |
+
- Docking simulation with binding energy results
|
| 10 |
+
- BSV blockchain verification display
|
| 11 |
+
|
| 12 |
+
Powered by: Origin Neural AI Docking Engine
|
| 13 |
+
Sponsored by: Smartledger Solutions, Origin Neural AI, Bryan Daugherty
|
| 14 |
+
Website: https://bioprime.one
|
| 15 |
+
"""
|
| 16 |
+
|
| 17 |
+
import gradio as gr
|
| 18 |
+
import py3Dmol
|
| 19 |
+
import requests
|
| 20 |
+
import json
|
| 21 |
+
import hashlib
|
| 22 |
+
import random
|
| 23 |
+
from datetime import datetime
|
| 24 |
+
from typing import Optional, Dict, List, Tuple
|
| 25 |
+
import time
|
| 26 |
+
|
| 27 |
+
# =============================================================================
|
| 28 |
+
# Configuration
|
| 29 |
+
# =============================================================================
|
| 30 |
+
|
| 31 |
+
BIOPRIME_API = "https://bioprime.one/api/v1"
|
| 32 |
+
RCSB_PDB_URL = "https://files.rcsb.org/download"
|
| 33 |
+
|
| 34 |
+
# Demo targets with sponsored research campaigns
|
| 35 |
+
DEMO_TARGETS = [
|
| 36 |
+
{
|
| 37 |
+
"id": "melanoma",
|
| 38 |
+
"name": "BRAF V600E - Melanoma",
|
| 39 |
+
"pdb": "4MNE",
|
| 40 |
+
"sponsor": "Bryan Daugherty",
|
| 41 |
+
"disease": "Melanoma",
|
| 42 |
+
"description": "Mutated BRAF kinase found in ~50% of melanomas, target for vemurafenib-like inhibitors.",
|
| 43 |
+
"binding_site": {"x": 25.0, "y": 5.0, "z": 15.0},
|
| 44 |
+
"color": "#FF6B6B"
|
| 45 |
+
},
|
| 46 |
+
{
|
| 47 |
+
"id": "diabetes",
|
| 48 |
+
"name": "DPP-4 - Type 2 Diabetes",
|
| 49 |
+
"pdb": "2ONC",
|
| 50 |
+
"sponsor": "Bryan Daugherty",
|
| 51 |
+
"disease": "Type 2 Diabetes",
|
| 52 |
+
"description": "Dipeptidyl peptidase-4, target for incretin-based diabetes medications like sitagliptin.",
|
| 53 |
+
"binding_site": {"x": 35.0, "y": 40.0, "z": 45.0},
|
| 54 |
+
"color": "#4ECDC4"
|
| 55 |
+
},
|
| 56 |
+
{
|
| 57 |
+
"id": "covid",
|
| 58 |
+
"name": "COVID-19 Main Protease",
|
| 59 |
+
"pdb": "6LU7",
|
| 60 |
+
"sponsor": "BioPrime Community",
|
| 61 |
+
"disease": "COVID-19",
|
| 62 |
+
"description": "SARS-CoV-2 main protease (Mpro), essential for viral replication. Target for Paxlovid.",
|
| 63 |
+
"binding_site": {"x": -10.8, "y": 35.2, "z": 63.4},
|
| 64 |
+
"color": "#9B59B6"
|
| 65 |
+
},
|
| 66 |
+
{
|
| 67 |
+
"id": "hiv",
|
| 68 |
+
"name": "HIV-1 Protease",
|
| 69 |
+
"pdb": "1HVR",
|
| 70 |
+
"sponsor": "Origin Neural AI",
|
| 71 |
+
"disease": "HIV/AIDS",
|
| 72 |
+
"description": "Critical enzyme for HIV replication, target for protease inhibitor antiretroviral drugs.",
|
| 73 |
+
"binding_site": {"x": -6.2, "y": 20.1, "z": 41.8},
|
| 74 |
+
"color": "#E74C3C"
|
| 75 |
+
},
|
| 76 |
+
{
|
| 77 |
+
"id": "lung",
|
| 78 |
+
"name": "EGFR Kinase - Lung Cancer",
|
| 79 |
+
"pdb": "1M17",
|
| 80 |
+
"sponsor": "Smartledger & Origin Neural AI",
|
| 81 |
+
"disease": "Non-small Cell Lung Cancer",
|
| 82 |
+
"description": "Epidermal growth factor receptor, key target in NSCLC therapy. Target for erlotinib.",
|
| 83 |
+
"binding_site": {"x": 40.5, "y": 0.6, "z": 56.0},
|
| 84 |
+
"color": "#3498DB"
|
| 85 |
+
},
|
| 86 |
+
{
|
| 87 |
+
"id": "breast",
|
| 88 |
+
"name": "CDK4/6 - Breast Cancer",
|
| 89 |
+
"pdb": "5L2I",
|
| 90 |
+
"sponsor": "Smartledger",
|
| 91 |
+
"disease": "Breast Cancer",
|
| 92 |
+
"description": "Cyclin-dependent kinase 4/6 inhibitor target for hormone-receptor positive breast cancer.",
|
| 93 |
+
"binding_site": {"x": 15.0, "y": 25.0, "z": 35.0},
|
| 94 |
+
"color": "#E91E63"
|
| 95 |
+
},
|
| 96 |
+
]
|
| 97 |
+
|
| 98 |
+
# Demo compound library
|
| 99 |
+
COMPOUND_LIBRARY = [
|
| 100 |
+
{"id": "aspirin", "name": "Aspirin", "smiles": "CC(=O)OC1=CC=CC=C1C(=O)O", "mw": 180.16, "category": "Anti-inflammatory"},
|
| 101 |
+
{"id": "ibuprofen", "name": "Ibuprofen", "smiles": "CC(C)CC1=CC=C(C=C1)C(C)C(=O)O", "mw": 206.29, "category": "Anti-inflammatory"},
|
| 102 |
+
{"id": "caffeine", "name": "Caffeine", "smiles": "CN1C=NC2=C1C(=O)N(C(=O)N2C)C", "mw": 194.19, "category": "Stimulant"},
|
| 103 |
+
{"id": "paracetamol", "name": "Acetaminophen", "smiles": "CC(=O)NC1=CC=C(O)C=C1", "mw": 151.16, "category": "Analgesic"},
|
| 104 |
+
{"id": "metformin", "name": "Metformin", "smiles": "CN(C)C(=N)NC(=N)N", "mw": 129.17, "category": "Antidiabetic"},
|
| 105 |
+
{"id": "atorvastatin", "name": "Atorvastatin", "smiles": "CC(C)C1=C(C(=C(N1CCC(CC(CC(=O)O)O)O)C2=CC=C(C=C2)F)C3=CC=CC=C3)C(=O)NC4=CC=CC=C4", "mw": 558.64, "category": "Statin"},
|
| 106 |
+
{"id": "nirmatrelvir", "name": "Nirmatrelvir", "smiles": "CC1(CC1)C(=O)NC(CC2CCNC2=O)C(=O)NC(CC(F)(F)F)C#N", "mw": 499.53, "category": "Antiviral (COVID-19)"},
|
| 107 |
+
{"id": "oseltamivir", "name": "Oseltamivir", "smiles": "CCOC(=O)C1=CC(OC(CC)CC)C(NC(C)=O)C(N)C1", "mw": 312.41, "category": "Antiviral (Flu)"},
|
| 108 |
+
{"id": "remdesivir", "name": "Remdesivir", "smiles": "CCC(CC)COC(=O)C(C)NP(=O)(OCC1C(C(C(O1)N2C=CC(=O)NC2=O)O)O)OC3=CC=CC=C3", "mw": 602.58, "category": "Antiviral"},
|
| 109 |
+
{"id": "sitagliptin", "name": "Sitagliptin", "smiles": "NC(CC(=O)N1CCN2C(C1)=NN=C2C(F)(F)F)CC1=C(F)C=C(F)C(F)=C1F", "mw": 407.31, "category": "Antidiabetic (DPP-4)"},
|
| 110 |
+
{"id": "vemurafenib", "name": "Vemurafenib", "smiles": "CCCS(=O)(=O)NC1=CC=C(C=C1)C2=NC(=C(S2)C3=CC(=NC=C3)NC4=CC=C(C=C4)Cl)C#N", "mw": 489.93, "category": "Kinase Inhibitor (Melanoma)"},
|
| 111 |
+
{"id": "erlotinib", "name": "Erlotinib", "smiles": "COCCOC1=C(C=C2C(=C1)C(=NC=N2)NC3=CC(=C(C=C3)F)Cl)OCCOC", "mw": 393.44, "category": "EGFR Inhibitor"},
|
| 112 |
+
]
|
| 113 |
+
|
| 114 |
+
# Pre-computed docking results (simulated but realistic)
|
| 115 |
+
PRECOMPUTED_RESULTS = {
|
| 116 |
+
"melanoma": {
|
| 117 |
+
"vemurafenib": -9.8,
|
| 118 |
+
"erlotinib": -7.2,
|
| 119 |
+
"caffeine": -4.1,
|
| 120 |
+
"aspirin": -5.3,
|
| 121 |
+
"ibuprofen": -5.8,
|
| 122 |
+
},
|
| 123 |
+
"diabetes": {
|
| 124 |
+
"sitagliptin": -10.2,
|
| 125 |
+
"metformin": -6.8,
|
| 126 |
+
"caffeine": -4.5,
|
| 127 |
+
"aspirin": -4.9,
|
| 128 |
+
"ibuprofen": -5.1,
|
| 129 |
+
},
|
| 130 |
+
"covid": {
|
| 131 |
+
"nirmatrelvir": -8.9,
|
| 132 |
+
"remdesivir": -7.6,
|
| 133 |
+
"caffeine": -5.2,
|
| 134 |
+
"aspirin": -4.8,
|
| 135 |
+
"oseltamivir": -6.4,
|
| 136 |
+
},
|
| 137 |
+
"hiv": {
|
| 138 |
+
"remdesivir": -7.8,
|
| 139 |
+
"oseltamivir": -6.2,
|
| 140 |
+
"caffeine": -4.3,
|
| 141 |
+
"aspirin": -4.5,
|
| 142 |
+
"atorvastatin": -6.9,
|
| 143 |
+
},
|
| 144 |
+
"lung": {
|
| 145 |
+
"erlotinib": -9.4,
|
| 146 |
+
"vemurafenib": -7.1,
|
| 147 |
+
"caffeine": -4.0,
|
| 148 |
+
"aspirin": -4.7,
|
| 149 |
+
"atorvastatin": -6.5,
|
| 150 |
+
},
|
| 151 |
+
"breast": {
|
| 152 |
+
"atorvastatin": -7.3,
|
| 153 |
+
"erlotinib": -6.8,
|
| 154 |
+
"caffeine": -4.2,
|
| 155 |
+
"aspirin": -4.4,
|
| 156 |
+
"metformin": -5.1,
|
| 157 |
+
},
|
| 158 |
+
}
|
| 159 |
+
|
| 160 |
+
# =============================================================================
|
| 161 |
+
# Helper Functions
|
| 162 |
+
# =============================================================================
|
| 163 |
+
|
| 164 |
+
def fetch_pdb_structure(pdb_id: str) -> Optional[str]:
|
| 165 |
+
"""Fetch PDB structure from RCSB."""
|
| 166 |
+
try:
|
| 167 |
+
# Try BioPrime API first
|
| 168 |
+
response = requests.get(f"{BIOPRIME_API}/docking/demo/pdb/{pdb_id}", timeout=10)
|
| 169 |
+
if response.status_code == 200:
|
| 170 |
+
data = response.json()
|
| 171 |
+
return data.get("pdb_content", data.get("pdb_data", None))
|
| 172 |
+
except:
|
| 173 |
+
pass
|
| 174 |
+
|
| 175 |
+
# Fallback to RCSB
|
| 176 |
+
try:
|
| 177 |
+
response = requests.get(f"{RCSB_PDB_URL}/{pdb_id}.pdb", timeout=10)
|
| 178 |
+
if response.status_code == 200:
|
| 179 |
+
return response.text
|
| 180 |
+
except:
|
| 181 |
+
pass
|
| 182 |
+
|
| 183 |
+
return None
|
| 184 |
+
|
| 185 |
+
|
| 186 |
+
def create_3d_viewer(pdb_content: str, binding_site: dict = None, style: str = "cartoon") -> str:
|
| 187 |
+
"""Create 3D molecular viewer HTML."""
|
| 188 |
+
view = py3Dmol.view(width=700, height=500)
|
| 189 |
+
view.addModel(pdb_content, "pdb")
|
| 190 |
+
|
| 191 |
+
if style == "cartoon":
|
| 192 |
+
view.setStyle({'cartoon': {'color': 'spectrum'}})
|
| 193 |
+
elif style == "surface":
|
| 194 |
+
view.setStyle({'cartoon': {'color': 'spectrum'}})
|
| 195 |
+
view.addSurface(py3Dmol.SAS, {'opacity': 0.7, 'color': 'white'})
|
| 196 |
+
elif style == "stick":
|
| 197 |
+
view.setStyle({'stick': {'colorscheme': 'Jmol'}})
|
| 198 |
+
elif style == "sphere":
|
| 199 |
+
view.setStyle({'sphere': {'colorscheme': 'Jmol', 'scale': 0.3}})
|
| 200 |
+
|
| 201 |
+
# Highlight binding site if provided
|
| 202 |
+
if binding_site:
|
| 203 |
+
view.addSphere({
|
| 204 |
+
'center': {'x': binding_site['x'], 'y': binding_site['y'], 'z': binding_site['z']},
|
| 205 |
+
'radius': 8,
|
| 206 |
+
'color': 'red',
|
| 207 |
+
'opacity': 0.3
|
| 208 |
+
})
|
| 209 |
+
|
| 210 |
+
view.zoomTo()
|
| 211 |
+
view.spin(False)
|
| 212 |
+
|
| 213 |
+
return view._make_html()
|
| 214 |
+
|
| 215 |
+
|
| 216 |
+
def generate_docking_result(target_id: str, compound_ids: List[str]) -> Tuple[str, str, str]:
|
| 217 |
+
"""
|
| 218 |
+
Simulate docking and return results.
|
| 219 |
+
Returns: (results_text, binding_chart_data, receipt)
|
| 220 |
+
"""
|
| 221 |
+
target = next((t for t in DEMO_TARGETS if t["id"] == target_id), None)
|
| 222 |
+
if not target:
|
| 223 |
+
return "Target not found", "", ""
|
| 224 |
+
|
| 225 |
+
results = []
|
| 226 |
+
precomputed = PRECOMPUTED_RESULTS.get(target_id, {})
|
| 227 |
+
|
| 228 |
+
for comp_id in compound_ids:
|
| 229 |
+
compound = next((c for c in COMPOUND_LIBRARY if c["id"] == comp_id), None)
|
| 230 |
+
if not compound:
|
| 231 |
+
continue
|
| 232 |
+
|
| 233 |
+
# Use precomputed or generate realistic random
|
| 234 |
+
if comp_id in precomputed:
|
| 235 |
+
energy = precomputed[comp_id]
|
| 236 |
+
else:
|
| 237 |
+
# Generate realistic binding energy based on molecular weight
|
| 238 |
+
base_energy = -4.0 - (compound["mw"] / 100)
|
| 239 |
+
energy = round(base_energy + random.uniform(-1.5, 1.5), 2)
|
| 240 |
+
|
| 241 |
+
results.append({
|
| 242 |
+
"compound": compound["name"],
|
| 243 |
+
"smiles": compound["smiles"],
|
| 244 |
+
"energy": energy,
|
| 245 |
+
"mw": compound["mw"],
|
| 246 |
+
"category": compound["category"]
|
| 247 |
+
})
|
| 248 |
+
|
| 249 |
+
# Sort by binding energy (more negative = better)
|
| 250 |
+
results.sort(key=lambda x: x["energy"])
|
| 251 |
+
|
| 252 |
+
# Generate results text
|
| 253 |
+
results_text = f"""
|
| 254 |
+
## Docking Results for {target['name']}
|
| 255 |
+
|
| 256 |
+
**Target Disease:** {target['disease']}
|
| 257 |
+
**Sponsor:** {target['sponsor']}
|
| 258 |
+
**PDB ID:** {target['pdb']}
|
| 259 |
+
|
| 260 |
+
---
|
| 261 |
+
|
| 262 |
+
### Top Binding Compounds
|
| 263 |
+
|
| 264 |
+
| Rank | Compound | Binding Energy | Category |
|
| 265 |
+
|------|----------|----------------|----------|
|
| 266 |
+
"""
|
| 267 |
+
|
| 268 |
+
for i, r in enumerate(results[:10], 1):
|
| 269 |
+
emoji = "🏆" if i == 1 else "🥈" if i == 2 else "🥉" if i == 3 else " "
|
| 270 |
+
results_text += f"| {emoji} {i} | **{r['compound']}** | {r['energy']:.2f} kcal/mol | {r['category']} |\n"
|
| 271 |
+
|
| 272 |
+
results_text += f"""
|
| 273 |
+
---
|
| 274 |
+
|
| 275 |
+
### Interpretation
|
| 276 |
+
|
| 277 |
+
- **Best Hit:** {results[0]['compound']} with {results[0]['energy']:.2f} kcal/mol
|
| 278 |
+
- **Binding energies < -7 kcal/mol** indicate strong binding potential
|
| 279 |
+
- **Binding energies < -9 kcal/mol** suggest drug-like affinity
|
| 280 |
+
|
| 281 |
+
---
|
| 282 |
+
|
| 283 |
+
*Powered by Origin Neural AI Docking Engine*
|
| 284 |
+
*Results simulated for demonstration - actual BioPrime uses GPU-accelerated physics*
|
| 285 |
+
"""
|
| 286 |
+
|
| 287 |
+
# Generate chart data
|
| 288 |
+
chart_labels = [r["compound"][:12] for r in results[:8]]
|
| 289 |
+
chart_values = [abs(r["energy"]) for r in results[:8]]
|
| 290 |
+
|
| 291 |
+
chart_html = f"""
|
| 292 |
+
<div style="background: linear-gradient(135deg, #1a1a2e 0%, #16213e 100%); padding: 20px; border-radius: 12px; margin-top: 10px;">
|
| 293 |
+
<h3 style="color: #4ECDC4; margin-bottom: 15px; text-align: center;">Binding Affinity Comparison</h3>
|
| 294 |
+
<div style="display: flex; align-items: flex-end; justify-content: space-around; height: 200px; padding: 10px;">
|
| 295 |
+
"""
|
| 296 |
+
|
| 297 |
+
max_val = max(chart_values) if chart_values else 1
|
| 298 |
+
colors = ["#FF6B6B", "#4ECDC4", "#45B7D1", "#96CEB4", "#FFEAA7", "#DDA0DD", "#98D8C8", "#F7DC6F"]
|
| 299 |
+
|
| 300 |
+
for i, (label, val) in enumerate(zip(chart_labels, chart_values)):
|
| 301 |
+
height = int((val / max_val) * 150)
|
| 302 |
+
color = colors[i % len(colors)]
|
| 303 |
+
chart_html += f"""
|
| 304 |
+
<div style="display: flex; flex-direction: column; align-items: center; width: 60px;">
|
| 305 |
+
<span style="color: white; font-size: 11px; margin-bottom: 5px;">-{val:.1f}</span>
|
| 306 |
+
<div style="width: 40px; height: {height}px; background: {color}; border-radius: 4px 4px 0 0;"></div>
|
| 307 |
+
<span style="color: #888; font-size: 9px; margin-top: 5px; text-align: center; word-wrap: break-word; width: 55px;">{label}</span>
|
| 308 |
+
</div>
|
| 309 |
+
"""
|
| 310 |
+
|
| 311 |
+
chart_html += """
|
| 312 |
+
</div>
|
| 313 |
+
<p style="color: #666; font-size: 11px; text-align: center; margin-top: 10px;">Binding Energy (kcal/mol) - Higher bars = stronger binding</p>
|
| 314 |
+
</div>
|
| 315 |
+
"""
|
| 316 |
+
|
| 317 |
+
# Generate blockchain receipt
|
| 318 |
+
job_id = f"DEMO-{target_id.upper()}-{hashlib.md5(str(compound_ids).encode()).hexdigest()[:8]}"
|
| 319 |
+
data_hash = hashlib.sha256(json.dumps(results, sort_keys=True).encode()).hexdigest()
|
| 320 |
+
|
| 321 |
+
receipt = generate_demo_receipt(
|
| 322 |
+
job_id=job_id,
|
| 323 |
+
target_name=target['name'],
|
| 324 |
+
compounds_screened=len(compound_ids),
|
| 325 |
+
top_hits=len(results),
|
| 326 |
+
best_energy=results[0]['energy'] if results else 0,
|
| 327 |
+
data_hash=data_hash
|
| 328 |
+
)
|
| 329 |
+
|
| 330 |
+
return results_text, chart_html, receipt
|
| 331 |
+
|
| 332 |
+
|
| 333 |
+
def generate_demo_receipt(job_id: str, target_name: str, compounds_screened: int,
|
| 334 |
+
top_hits: int, best_energy: float, data_hash: str) -> str:
|
| 335 |
+
"""Generate a demo blockchain receipt."""
|
| 336 |
+
timestamp = datetime.utcnow().strftime("%Y-%m-%d %H:%M:%S UTC")
|
| 337 |
+
demo_txid = f"demo_{hashlib.md5(data_hash.encode()).hexdigest()[:48]}"
|
| 338 |
+
|
| 339 |
+
receipt = f"""
|
| 340 |
+
╔══════════════════════════════════════════════════════════════════════════╗
|
| 341 |
+
║ BIOPRIME DISCOVERY CERTIFICATE ║
|
| 342 |
+
║ [DEMO - NOT ON CHAIN] ║
|
| 343 |
+
╠══════════════════════════════════════════════════════════════════════════╣
|
| 344 |
+
║ ║
|
| 345 |
+
║ JOB ID: {job_id:<57} ║
|
| 346 |
+
║ TARGET: {target_name[:47]:<57} ║
|
| 347 |
+
║ ║
|
| 348 |
+
╠══════════════════════════════════════════════════════════════════════════╣
|
| 349 |
+
║ SCREENING RESULTS ║
|
| 350 |
+
╠══════════════════════════════════════════════════════════════════════════╣
|
| 351 |
+
║ ║
|
| 352 |
+
║ Compounds Screened: {compounds_screened:<45} ║
|
| 353 |
+
║ Top Poses Generated: {top_hits:<45} ║
|
| 354 |
+
║ Best Binding Energy: {best_energy:.2f} kcal/mol{' ':<36} ║
|
| 355 |
+
║ ║
|
| 356 |
+
╠══════════════════════════════════════════════════════════════════════════╣
|
| 357 |
+
║ VERIFICATION DETAILS ║
|
| 358 |
+
╠══════════════════════════════════════════════════════════════════════════╣
|
| 359 |
+
║ ║
|
| 360 |
+
║ Timestamp: {timestamp:<53} ║
|
| 361 |
+
║ Data Hash: sha256:{data_hash[:49]:<46} ║
|
| 362 |
+
║ ║
|
| 363 |
+
╠══════════════════════════════════════════════════════════════════════════╣
|
| 364 |
+
║ BLOCKCHAIN VERIFICATION ║
|
| 365 |
+
╠══════════════════════════════════════════════════════════════════════════╣
|
| 366 |
+
║ ║
|
| 367 |
+
║ Network: BSV (Bitcoin SV) - Demo Mode ║
|
| 368 |
+
║ Status: Demo certificate - not anchored to blockchain ║
|
| 369 |
+
║ ║
|
| 370 |
+
║ For real blockchain-verified results, visit: ║
|
| 371 |
+
║ https://bioprime.one ║
|
| 372 |
+
║ ║
|
| 373 |
+
╠══════════════════════════════════════════════════════════════════════════╣
|
| 374 |
+
║ ║
|
| 375 |
+
║ BioPrime anchors real docking results to the BSV blockchain for ║
|
| 376 |
+
║ immutable proof of discovery. Sign up to run verified experiments. ║
|
| 377 |
+
║ ║
|
| 378 |
+
║ ━━━ bioprime.one ━━━ ║
|
| 379 |
+
║ ║
|
| 380 |
+
╚══════════════════════════════════════════════════════════════════════════╝
|
| 381 |
+
"""
|
| 382 |
+
return receipt.strip()
|
| 383 |
+
|
| 384 |
+
|
| 385 |
+
# =============================================================================
|
| 386 |
+
# Gradio Interface
|
| 387 |
+
# =============================================================================
|
| 388 |
+
|
| 389 |
+
def view_protein(target_name: str, view_style: str) -> Tuple[str, str]:
|
| 390 |
+
"""View selected protein structure."""
|
| 391 |
+
target = next((t for t in DEMO_TARGETS if t["name"] == target_name), None)
|
| 392 |
+
if not target:
|
| 393 |
+
return "<p>Please select a target</p>", ""
|
| 394 |
+
|
| 395 |
+
pdb_content = fetch_pdb_structure(target["pdb"])
|
| 396 |
+
if not pdb_content:
|
| 397 |
+
return f"<p style='color: red;'>Failed to fetch PDB structure for {target['pdb']}</p>", ""
|
| 398 |
+
|
| 399 |
+
viewer_html = create_3d_viewer(pdb_content, target.get("binding_site"), view_style.lower())
|
| 400 |
+
|
| 401 |
+
info_html = f"""
|
| 402 |
+
<div style="background: linear-gradient(135deg, #0f0c29 0%, #302b63 50%, #24243e 100%); padding: 20px; border-radius: 12px; color: white;">
|
| 403 |
+
<h3 style="color: {target['color']}; margin-bottom: 10px;">{target['name']}</h3>
|
| 404 |
+
<p><strong>PDB ID:</strong> <a href="https://www.rcsb.org/structure/{target['pdb']}" target="_blank" style="color: #4ECDC4;">{target['pdb']}</a></p>
|
| 405 |
+
<p><strong>Disease:</strong> {target['disease']}</p>
|
| 406 |
+
<p><strong>Sponsor:</strong> {target['sponsor']}</p>
|
| 407 |
+
<p style="margin-top: 10px; color: #aaa;">{target['description']}</p>
|
| 408 |
+
<div style="margin-top: 15px; padding: 10px; background: rgba(78, 205, 196, 0.1); border-radius: 8px; border-left: 3px solid #4ECDC4;">
|
| 409 |
+
<p style="font-size: 12px; color: #4ECDC4; margin: 0;">
|
| 410 |
+
💡 The red sphere indicates the active binding site where drug candidates interact with the protein.
|
| 411 |
+
</p>
|
| 412 |
+
</div>
|
| 413 |
+
</div>
|
| 414 |
+
"""
|
| 415 |
+
|
| 416 |
+
return viewer_html, info_html
|
| 417 |
+
|
| 418 |
+
|
| 419 |
+
def run_docking(target_name: str, compounds: List[str], progress=gr.Progress()) -> Tuple[str, str, str]:
|
| 420 |
+
"""Run docking simulation."""
|
| 421 |
+
if not target_name:
|
| 422 |
+
return "Please select a target protein", "", ""
|
| 423 |
+
if not compounds:
|
| 424 |
+
return "Please select at least one compound", "", ""
|
| 425 |
+
|
| 426 |
+
target = next((t for t in DEMO_TARGETS if t["name"] == target_name), None)
|
| 427 |
+
if not target:
|
| 428 |
+
return "Invalid target", "", ""
|
| 429 |
+
|
| 430 |
+
# Get compound IDs from names
|
| 431 |
+
compound_ids = []
|
| 432 |
+
for comp_name in compounds:
|
| 433 |
+
comp = next((c for c in COMPOUND_LIBRARY if c["name"] == comp_name), None)
|
| 434 |
+
if comp:
|
| 435 |
+
compound_ids.append(comp["id"])
|
| 436 |
+
|
| 437 |
+
# Simulate docking progress
|
| 438 |
+
progress(0, desc="Initializing docking engine...")
|
| 439 |
+
time.sleep(0.5)
|
| 440 |
+
|
| 441 |
+
progress(0.2, desc="Loading protein structure...")
|
| 442 |
+
time.sleep(0.3)
|
| 443 |
+
|
| 444 |
+
progress(0.4, desc="Preparing compound library...")
|
| 445 |
+
time.sleep(0.3)
|
| 446 |
+
|
| 447 |
+
progress(0.6, desc="Running molecular docking...")
|
| 448 |
+
time.sleep(0.5)
|
| 449 |
+
|
| 450 |
+
progress(0.8, desc="Analyzing binding poses...")
|
| 451 |
+
time.sleep(0.3)
|
| 452 |
+
|
| 453 |
+
progress(0.95, desc="Generating results...")
|
| 454 |
+
results_text, chart_html, receipt = generate_docking_result(target["id"], compound_ids)
|
| 455 |
+
|
| 456 |
+
progress(1.0, desc="Complete!")
|
| 457 |
+
|
| 458 |
+
return results_text, chart_html, receipt
|
| 459 |
+
|
| 460 |
+
|
| 461 |
+
# Create the Gradio interface
|
| 462 |
+
with gr.Blocks(
|
| 463 |
+
title="BioPrime Molecular Docking Demo",
|
| 464 |
+
theme=gr.themes.Base(
|
| 465 |
+
primary_hue="teal",
|
| 466 |
+
secondary_hue="purple",
|
| 467 |
+
neutral_hue="slate",
|
| 468 |
+
font=gr.themes.GoogleFont("Inter")
|
| 469 |
+
),
|
| 470 |
+
css="""
|
| 471 |
+
.gradio-container {
|
| 472 |
+
max-width: 1400px !important;
|
| 473 |
+
background: linear-gradient(135deg, #0f0c29 0%, #302b63 50%, #24243e 100%) !important;
|
| 474 |
+
}
|
| 475 |
+
.gr-button-primary {
|
| 476 |
+
background: linear-gradient(135deg, #4ECDC4 0%, #44A08D 100%) !important;
|
| 477 |
+
}
|
| 478 |
+
.header-text {
|
| 479 |
+
text-align: center;
|
| 480 |
+
color: white;
|
| 481 |
+
}
|
| 482 |
+
footer {display: none !important;}
|
| 483 |
+
"""
|
| 484 |
+
) as demo:
|
| 485 |
+
|
| 486 |
+
# Header
|
| 487 |
+
gr.HTML("""
|
| 488 |
+
<div style="text-align: center; padding: 20px; background: linear-gradient(135deg, #667eea 0%, #764ba2 100%); border-radius: 12px; margin-bottom: 20px;">
|
| 489 |
+
<h1 style="color: white; margin: 0; font-size: 2.5em;">🧬 BioPrime</h1>
|
| 490 |
+
<p style="color: rgba(255,255,255,0.9); margin: 10px 0 0 0; font-size: 1.2em;">
|
| 491 |
+
AI-Powered Molecular Docking for Drug Discovery
|
| 492 |
+
</p>
|
| 493 |
+
<p style="color: rgba(255,255,255,0.7); margin: 5px 0 0 0;">
|
| 494 |
+
10,000x Faster • $5 per Million Compounds • Blockchain-Verified Results
|
| 495 |
+
</p>
|
| 496 |
+
</div>
|
| 497 |
+
""")
|
| 498 |
+
|
| 499 |
+
with gr.Tabs():
|
| 500 |
+
# Tab 1: Interactive Docking Demo
|
| 501 |
+
with gr.TabItem("🔬 Try Docking", id="docking"):
|
| 502 |
+
gr.Markdown("""
|
| 503 |
+
### Dock Drug Candidates Against Disease Targets
|
| 504 |
+
Select a protein target and compounds to simulate molecular docking. See binding energies and get a blockchain-ready certificate.
|
| 505 |
+
""")
|
| 506 |
+
|
| 507 |
+
with gr.Row():
|
| 508 |
+
with gr.Column(scale=1):
|
| 509 |
+
target_dropdown = gr.Dropdown(
|
| 510 |
+
choices=[t["name"] for t in DEMO_TARGETS],
|
| 511 |
+
label="🎯 Select Disease Target",
|
| 512 |
+
info="Choose from sponsored research targets"
|
| 513 |
+
)
|
| 514 |
+
|
| 515 |
+
compound_select = gr.CheckboxGroup(
|
| 516 |
+
choices=[c["name"] for c in COMPOUND_LIBRARY],
|
| 517 |
+
label="💊 Select Compounds to Test",
|
| 518 |
+
info="Choose multiple compounds for screening"
|
| 519 |
+
)
|
| 520 |
+
|
| 521 |
+
dock_btn = gr.Button("🚀 Run Docking Simulation", variant="primary", size="lg")
|
| 522 |
+
|
| 523 |
+
gr.HTML("""
|
| 524 |
+
<div style="margin-top: 15px; padding: 15px; background: rgba(78, 205, 196, 0.1); border-radius: 8px; border: 1px solid rgba(78, 205, 196, 0.3);">
|
| 525 |
+
<h4 style="color: #4ECDC4; margin: 0 0 10px 0;">💡 Quick Start</h4>
|
| 526 |
+
<ol style="color: #aaa; margin: 0; padding-left: 20px; font-size: 13px;">
|
| 527 |
+
<li>Select <strong>BRAF V600E - Melanoma</strong></li>
|
| 528 |
+
<li>Check <strong>Vemurafenib</strong> (the actual drug!)</li>
|
| 529 |
+
<li>Add a few other compounds to compare</li>
|
| 530 |
+
<li>Click Run Docking</li>
|
| 531 |
+
</ol>
|
| 532 |
+
</div>
|
| 533 |
+
""")
|
| 534 |
+
|
| 535 |
+
with gr.Column(scale=2):
|
| 536 |
+
results_md = gr.Markdown("*Results will appear here after docking...*")
|
| 537 |
+
chart_html = gr.HTML()
|
| 538 |
+
|
| 539 |
+
with gr.Accordion("📜 Blockchain Certificate (Demo)", open=False):
|
| 540 |
+
receipt_text = gr.Code(label="Discovery Certificate", language=None, lines=30)
|
| 541 |
+
|
| 542 |
+
dock_btn.click(
|
| 543 |
+
fn=run_docking,
|
| 544 |
+
inputs=[target_dropdown, compound_select],
|
| 545 |
+
outputs=[results_md, chart_html, receipt_text]
|
| 546 |
+
)
|
| 547 |
+
|
| 548 |
+
# Tab 2: 3D Protein Viewer
|
| 549 |
+
with gr.TabItem("🔮 3D Protein Viewer", id="viewer"):
|
| 550 |
+
gr.Markdown("""
|
| 551 |
+
### Explore Protein Structures in 3D
|
| 552 |
+
Visualize the molecular targets for drug discovery. The red sphere indicates the binding site.
|
| 553 |
+
""")
|
| 554 |
+
|
| 555 |
+
with gr.Row():
|
| 556 |
+
with gr.Column(scale=1):
|
| 557 |
+
viewer_target = gr.Dropdown(
|
| 558 |
+
choices=[t["name"] for t in DEMO_TARGETS],
|
| 559 |
+
label="🎯 Select Protein",
|
| 560 |
+
value=DEMO_TARGETS[0]["name"]
|
| 561 |
+
)
|
| 562 |
+
|
| 563 |
+
view_style = gr.Radio(
|
| 564 |
+
choices=["Cartoon", "Surface", "Stick", "Sphere"],
|
| 565 |
+
value="Cartoon",
|
| 566 |
+
label="🎨 Visualization Style"
|
| 567 |
+
)
|
| 568 |
+
|
| 569 |
+
view_btn = gr.Button("👁️ View Structure", variant="primary")
|
| 570 |
+
|
| 571 |
+
target_info = gr.HTML()
|
| 572 |
+
|
| 573 |
+
with gr.Column(scale=2):
|
| 574 |
+
viewer_output = gr.HTML(
|
| 575 |
+
value="<div style='height: 500px; display: flex; align-items: center; justify-content: center; color: #666; background: #1a1a2e; border-radius: 12px;'><p>Select a protein and click 'View Structure'</p></div>"
|
| 576 |
+
)
|
| 577 |
+
|
| 578 |
+
view_btn.click(
|
| 579 |
+
fn=view_protein,
|
| 580 |
+
inputs=[viewer_target, view_style],
|
| 581 |
+
outputs=[viewer_output, target_info]
|
| 582 |
+
)
|
| 583 |
+
|
| 584 |
+
# Tab 3: About BioPrime
|
| 585 |
+
with gr.TabItem("ℹ️ About", id="about"):
|
| 586 |
+
gr.Markdown("""
|
| 587 |
+
## About BioPrime Network
|
| 588 |
+
|
| 589 |
+
BioPrime is a **decentralized molecular docking platform** that makes drug discovery accessible to everyone.
|
| 590 |
+
|
| 591 |
+
### Key Features
|
| 592 |
+
|
| 593 |
+
| Feature | Traditional | BioPrime |
|
| 594 |
+
|---------|-------------|----------|
|
| 595 |
+
| Speed | Days-Weeks | Minutes |
|
| 596 |
+
| Cost | $10,000+ | $5/million |
|
| 597 |
+
| Verification | Manual | Blockchain |
|
| 598 |
+
| Access | Limited | Open |
|
| 599 |
+
|
| 600 |
+
### How It Works
|
| 601 |
+
|
| 602 |
+
1. **Submit** - Upload your protein target or select from our library
|
| 603 |
+
2. **Screen** - Our Origin Neural AI engine docks millions of compounds
|
| 604 |
+
3. **Discover** - Get ranked binding poses with energy scores
|
| 605 |
+
4. **Verify** - Results anchored to BSV blockchain for immutable proof
|
| 606 |
+
|
| 607 |
+
### Sponsored Research Campaigns
|
| 608 |
+
|
| 609 |
+
BioPrime features sponsored research targets where community members can contribute to drug discovery:
|
| 610 |
+
|
| 611 |
+
- **Bryan Daugherty** - Melanoma (BRAF V600E), Type 2 Diabetes (DPP-4)
|
| 612 |
+
- **Smartledger** - Breast Cancer (CDK4/6)
|
| 613 |
+
- **Origin Neural AI** - HIV-1 Protease
|
| 614 |
+
- **Greg Ward** - Tuberculosis, Dengue Fever
|
| 615 |
+
- **Shawn Ryan** - Alzheimer's, Parkinson's
|
| 616 |
+
|
| 617 |
+
### Technology Stack
|
| 618 |
+
|
| 619 |
+
- **Docking Engine**: Origin Neural AI (GPU-accelerated)
|
| 620 |
+
- **Blockchain**: BSV (Bitcoin SV) for immutable verification
|
| 621 |
+
- **Backend**: FastAPI, Python
|
| 622 |
+
- **Frontend**: React, TypeScript
|
| 623 |
+
|
| 624 |
+
---
|
| 625 |
+
|
| 626 |
+
### Get Started
|
| 627 |
+
|
| 628 |
+
**🌐 Visit [bioprime.one](https://bioprime.one) to run real docking experiments!**
|
| 629 |
+
|
| 630 |
+
- Sign up for free (10 free credits)
|
| 631 |
+
- Screen up to 1 million compounds per job
|
| 632 |
+
- Get blockchain-verified discovery certificates
|
| 633 |
+
- Participate in sponsored research campaigns
|
| 634 |
+
|
| 635 |
+
---
|
| 636 |
+
|
| 637 |
+
<div style="text-align: center; padding: 20px; background: linear-gradient(135deg, #667eea 0%, #764ba2 100%); border-radius: 12px;">
|
| 638 |
+
<p style="color: white; font-size: 1.2em; margin: 0;">
|
| 639 |
+
<strong>Ready to discover the next breakthrough drug?</strong>
|
| 640 |
+
</p>
|
| 641 |
+
<p style="color: rgba(255,255,255,0.8); margin: 10px 0 0 0;">
|
| 642 |
+
<a href="https://bioprime.one" target="_blank" style="color: #4ECDC4; text-decoration: none; font-size: 1.3em;">
|
| 643 |
+
🚀 Launch BioPrime →
|
| 644 |
+
</a>
|
| 645 |
+
</p>
|
| 646 |
+
</div>
|
| 647 |
+
""")
|
| 648 |
+
|
| 649 |
+
# Footer
|
| 650 |
+
gr.HTML("""
|
| 651 |
+
<div style="text-align: center; padding: 20px; margin-top: 20px; border-top: 1px solid rgba(255,255,255,0.1);">
|
| 652 |
+
<p style="color: #666; margin: 0;">
|
| 653 |
+
<a href="https://bioprime.one" target="_blank" style="color: #4ECDC4;">bioprime.one</a> •
|
| 654 |
+
<a href="https://twitter.com/BioPrimeNetwork" target="_blank" style="color: #4ECDC4;">@BioPrimeNetwork</a> •
|
| 655 |
+
<a href="https://github.com/bioprime-network" target="_blank" style="color: #4ECDC4;">GitHub</a>
|
| 656 |
+
</p>
|
| 657 |
+
<p style="color: #444; margin: 5px 0 0 0; font-size: 12px;">
|
| 658 |
+
Powered by Origin Neural AI • Blockchain verification on BSV
|
| 659 |
+
</p>
|
| 660 |
+
</div>
|
| 661 |
+
""")
|
| 662 |
+
|
| 663 |
+
|
| 664 |
+
if __name__ == "__main__":
|
| 665 |
+
demo.launch()
|