PandaDock: An Open-Source Molecular Docking Platform with Flexible-Ligand Search and Equivariant Neural Scoring
We present PandaDock, an open-source molecular docking platform implementing flexible-ligand conformational search with analytic gradients, a precomputed affinity grid engine, specialized modules for induced-fit, metal-coordination and tethered docking, and an SE(3)-equivariant graph neural network scoring function trained at scale. Ligand flexibility is represented as a torsion tree and pose…
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