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Our system architecture represents a fundamental innovation in integrating multiple data sources. We work with 17 high-quality CYP enzyme structures - 8 for CYP3A4, 6 for CYP2D6, and 3 for CYP2C19. Each enzyme includes one AlphaFold prediction combined with experimental PDB structures, giving us 100% structural coverage. The dual embedding pipeline is the heart of our innovation. We generate 384-dimensional text embeddings using Sentence-BERT for semantic understanding, and 256-dimensional geometric embeddings that capture structural features including curvature, distances, residue types, and electrostatics. The key innovation is our hybrid retrieval formula: S_hybrid equals alpha times S_text plus one minus alpha times S_geometric. Through extensive experimentation, we found the optimal alpha value is 0.7, meaning we weight text information at 70% and structural information at 30%. This is the first system to mathematically combine semantic and spatial protein information for enhanced retrieval accuracy. |
IEEE/ICACT20260263 Slide.05
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