Advanced chemical oxidation treatment of dye wastewater and

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5 A˚ to about 37 A The lowest RMSD structures were from the data set that used flexible side chains. The authors also found that electrostatic interactions play a primary role in finding the correct binding site and orientation of the peptide. Simulations without electrostatic interactions yielded significantly poorer structural predictions. Overall the authors concluded that using a protocol that allows flexible side chains and includes electrostatic interactions greatly improves the protein–peptide complex prediction.

Medina-Franco, J. L. (2012). Molecular modeling of inhibitors of human DNA methyltransferase with a crystal structure: Discovery of a novel DNMT1 inhibitor. Advances in Protein Chemistry and Structure Biology, 87, 219–247. 00008-1. , & Medina-Franco, J. L. (2011). Homology modeling, docking, and structure-based pharmacophore of inhibitors of DNA methyltransferase. Journal of Computer-Aided Molecular Design, 25(6), 555–567. 1007/s10822-011-9441-1. , & Medina-Franco, J. L. (2012). Inhibitors of DNA methyltransferases: Insights from computational studies.

However, these analogs contain nonnatural amino acids and/or adducts. With this in mind, Rashid et al. (2013) set out to identify a selective ShK analog composed of only natural amino acids by means of FEP and thermodynamic integration (TI) calculations to evaluate the binding free energy changes associated with introducing mutations. Rashid et al. 3 receptors using PMF methods (Deng & Roux, 2009). , 1996; Rauer, Pennington, Cahalan, & Chandy, 1999) provided a starting point for the computational work of Rashid et al.

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