Topoisomerase II-DNA Crossover Recognition

Shin and Kim [39] used the accessible surface area of essential amino acid residues of the amine pyruvate aminotransferase and various amino donors and acceptors to explore the active site structure. Their results suggested a model consisting of two pockets, one large and the other small. The size difference between the binding pockets and the strong repulsion for a carboxylate in the small pocket were key determinants of the substrate specificity and stereoselectivity. 

HIV-1 reverse transcripase modeled the potency of chiral halopyridyl and tiazolyl 

The chemical databases used in docking are usually stereochemically defined within their 3D coordinates. Enantiomers are not stored. If it is necessary to invert the chiral centers for compound entry in the database, specific scripts using the function invert chiral centers should be applied. This enlarges fhe database significantly. 

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