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RMSD values are calculated relative to the top mode and use only movable weighty atoms. Two variants of RMSD metrics are supplied, rmsd/lb (RMSD lessen certain) and rmsd/ub (RMSD higher bound), differing in how the atoms are matched in the distance calculation:
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The research Room proficiently restricts where by the movable atoms, including Those people during the versatile side chains, must lie.
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Vina’s style and design philosophy is never to need the consumer to be aware of its implementation details, tweak obscure research parameters, cluster results or know State-of-the-art algebra (quaternions). All that is needed is definitely the constructions with the molecules becoming docked plus the specification with the search Room such as the binding website.
AccuracyAutoDock Vina considerably increases the typical accuracy of your binding mode predictions as compared to AutoDock 4, judging by our assessments over the instruction established Employed in AutoDock four improvement.[*]
By structure, the outcome should not Use a statistical bias linked to the conformation of the input structure.
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