3D_Search

The 3DPharmacoMatch module enables highly accurate virtual screening by leveraging the 3D conformational and key functional group features of known active molecules. This approach falls under structure-based drug design (SBDD) and emphasizes pharmacophore pattern recognition and steric/electronic compatibility rather than full flexible docking.

Using active molecules as templates, the algorithm performs rapid 3D similarity search and substructure-based alignment across large compound libraries. It evaluates candidates based on multi-dimensional criteria including molecular shape overlap, hydrogen bonding propensity, hydrophobic complementarity, and aromatic stacking potential.

By focusing on essential interaction features rather than full atomic detail, 3DPharmacoMatch achieves a significant boost in screening efficiency while maintaining high specificity. This feature-sensitive design dramatically increases enrichment rates and reduces computational cost, making it ideal for early-stage lead discovery and scaffold hopping. The module has been validated to show a 3–5× improvement in hit selection quality compared to conventional fingerprint-based or rigid docking methods.