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Abstract Protein structure prediction and protein docking prediction are two related problems in molecular biology. We suggest the use of multiple docking in the process of protein structure prediction. Once [...]

All-atom molecular dynamics simulations are performed on the unphosphorylated and phosphorylated unbound glycogen synthase kinase 3[beta] (GSK-3[beta]) and the phosphorylated GSK-3[beta] bound to a peptide substrate, its product, and a derived inhibitor. The studies have shown that binding of specific peptides at the remote binding site has led to stabilization of the activation loop located in the active site, which might enhance the catalytic activity of the kinase.

The studies which demonstrate the impact of binding two molecules of diazepam on the properties of human cytochrome P450 3A4 (CYP3A4) regulated by high-valent iron-oxo species (Cpd I) is reported.

The impact of the addition of an effector diazepam molecule on an active oxidized diazepam in the active site of CYP3A4 and on the interactions of the effector with the protein is investigated. The results indicate that the effector substrate interacts both with the active substrate and with the enzyme, which results in side chain reorientation with relatively minor long-range effects.