Esented in Fig 3A. The compounds are ranked according to pharmacological and energy-based scoring function. E, H and V indicate electrostatic, hydrogen bonding and vdW interactions, respectively. The vdW interactions are coloured in green when the energy is less than -4. The hydrogen bonding and electrostatic interactions are coloured in green if the energy is # 24. M and S indicates main chain or side chain of interacting residues. The residues showing important hydrogen bonding interactions with docked compounds is given in Fig. 3B. Hydrogen bonds are represented as green dashed lines A two dimensional figure of binding of compounds with PAZ domain is shown in 12926553 Fig. 3C. The ligand is compound tt, residues sharing with hydrogen bonding is shown in pink. doi:10.1371/journal.pone.0057140.gsiRNA Recognition by PAZ DomainFigure 4. Dissection of the PAZ domain-ligands interaction forces (data is obtained from the docking server). Free energy (Kcal/mol), inhibition constant (mM), van der Waals interactions, hydrogen bonding and desolvation energy (Kcal/mol), electrostatic energy (Kcal/mol) and interaction surface were plotted against RL/FL (Renilla luciferace expression normalized by firefly 114311-32-9 luciferase data). doi:10.1371/journal.pone.0057140.gwith higher 
Ki values. In Fig. 4B compounds with higher Ki values are associated with lower in vivo efficacy. Electrostatic interactions: From Table 1 electrostatic interactions are not a major contributor to the binding of compounds with the PAZ domain. Hydrogen bonding and van der Waals interactions are the major contributors to compounds recognition by the PAZ domain. Phosphate groups of natural nucleotides are the main source of electrostatic interactions with the cavity of the PAZ domain (Fig. 5). We found a moderate correlation between RNAi efficacy and electrostatic interactions (R = 0.22). Thus, we predict that modifying phosphate groups will not lead to major changes in compounds binding. In addition, their modification to other groups would be recommended if nuclease or phosphatase resistance is an obstacle to a compound’s RNAi activity.Furthermore, electrostatic interactions showed little changes among compounds. Total 
interaction surface: the interaction surface reflects the size of compounds and the area of the interaction surface with receptors. A higher area of interaction surface is associated with lower RNAi. RNAi efficacy was moderately-to-highly correlated with the interaction surface of the PAZ domain (R = 0.58, statistically significant at 0.05 level, Table 4). In agreement with the previously described work, this result suggests that smaller compounds are preferable for RNAi [10]. van der Waals and hydrogen bonding: these interactions contribute to the free energy of receptor-ligands binding, furthermore they stabilizes the binding process via association between electrically charged components of ligand-receptor complex. Higher RNAi was associated with lower van der Waals and hydrogen bondingsiRNA Recognition by PAZ DomainFigure 5. Electrostatic interactions of siRNA with PAZ domain. The phosphate groups of siRNA are marked by red Tetracosactrin site colour opposing the surface of PAZ domain in blue. doi:10.1371/journal.pone.0057140.ginteraction (Fig. 4E). RNAi efficacy was negatively correlated with the van der Waals interactions with the PAZ domain (R = 20.42, statistically significant at 0.05 level, Table 3). Results from iGEMDOCK are shown in Fig. 6. In a rough analysis of the figure, we concluded.Esented in Fig 3A. The compounds are ranked according to pharmacological and energy-based scoring function. E, H and V indicate electrostatic, hydrogen bonding and vdW interactions, respectively. The vdW interactions are coloured in green when the energy is less than -4. The hydrogen bonding and electrostatic interactions are coloured in green if the energy is # 24. M and S indicates main chain or side chain of interacting residues. The residues showing important hydrogen bonding interactions with docked compounds is given in Fig. 3B. Hydrogen bonds are represented as green dashed lines A two dimensional figure of binding of compounds with PAZ domain is shown in 12926553 Fig. 3C. The ligand is compound tt, residues sharing with hydrogen bonding is shown in pink. doi:10.1371/journal.pone.0057140.gsiRNA Recognition by PAZ DomainFigure 4. Dissection of the PAZ domain-ligands interaction forces (data is obtained from the docking server). Free energy (Kcal/mol), inhibition constant (mM), van der Waals interactions, hydrogen bonding and desolvation energy (Kcal/mol), electrostatic energy (Kcal/mol) and interaction surface were plotted against RL/FL (Renilla luciferace expression normalized by firefly luciferase data). doi:10.1371/journal.pone.0057140.gwith higher Ki values. In Fig. 4B compounds with higher Ki values are associated with lower in vivo efficacy. Electrostatic interactions: From Table 1 electrostatic interactions are not a major contributor to the binding of compounds with the PAZ domain. Hydrogen bonding and van der Waals interactions are the major contributors to compounds recognition by the PAZ domain. Phosphate groups of natural nucleotides are the main source of electrostatic interactions with the cavity of the PAZ domain (Fig. 5). We found a moderate correlation between RNAi efficacy and electrostatic interactions (R = 0.22). Thus, we predict that modifying phosphate groups will not lead to major changes in compounds binding. In addition, their modification to other groups would be recommended if nuclease or phosphatase resistance is an obstacle to a compound’s RNAi activity.Furthermore, electrostatic interactions showed little changes among compounds. Total interaction surface: the interaction surface reflects the size of compounds and the area of the interaction surface with receptors. A higher area of interaction surface is associated with lower RNAi. RNAi efficacy was moderately-to-highly correlated with the interaction surface of the PAZ domain (R = 0.58, statistically significant at 0.05 level, Table 4). In agreement with the previously described work, this result suggests that smaller compounds are preferable for RNAi [10]. van der Waals and hydrogen bonding: these interactions contribute to the free energy of receptor-ligands binding, furthermore they stabilizes the binding process via association between electrically charged components of ligand-receptor complex. Higher RNAi was associated with lower van der Waals and hydrogen bondingsiRNA Recognition by PAZ DomainFigure 5. Electrostatic interactions of siRNA with PAZ domain. The phosphate groups of siRNA are marked by red colour opposing the surface of PAZ domain in blue. doi:10.1371/journal.pone.0057140.ginteraction (Fig. 4E). RNAi efficacy was negatively correlated with the van der Waals interactions with the PAZ domain (R = 20.42, statistically significant at 0.05 level, Table 3). Results from iGEMDOCK are shown in Fig. 6. In a rough analysis of the figure, we concluded.