3D
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AutoDock-SS: AutoDock-SS enhances AutoDock for multiconformational and flexible ligand docking, considering various ligand conformations for accurate docking predictions.
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ROSHAMBO: Open-Source Molecular Alignment and 3D Similarity Scoring
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SCRdkit: assesses the 3D similarity between generated molecules and a reference molecule
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SENSAAS: SENSAAS is a shape-based alignment software for superimposing molecules, utilizing a colored point-based surface representation for molecular comparison.
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ShaEP: ShaEP aligns two 3D molecular structures and computes a similarity index, useful for virtual screening and 3D QSAR methods.