AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

Trott, Oleg, Olson, Arthur J.·2010·Journal of Computational Chemistry

Cited by (1,086)

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  89. Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening
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  93. Use of machine learning approaches for novel drug discovery
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