Autodock tools

Genetic algorithm (LGA) and the docked complex result found in the docking study is shown in Fig. 13 [27, 55, 95]. The binding energy was found to be − 12.82 kcal/mol and the molecular interaction was because of two hydrogen bonds formed with bond length 2.68 and 2.66 Å and three hydrophobic interactions with bond length 4.89, 5.46, and 5.75 Å.Fig. 13Organic–inorganic-hybrid MOF—organic dye molecule complex [112]. Complex structure of congo red dye (CR) (yellow color) with UiO-66 (a Zr (IV) based metal organic framework (MOF)) (gray and red) using ball-and-stick representation after docking study using AutoDock Vina [55, 95]. The active site is shown in cyan color ellipse [112]. (Color figure online)Full size imagePanda J et al. have demonstrated that ZIF-8 MOF can be used to remove reactive blue-4 (RB4), a reactive triazine toxic dye from water because of the absorption property of ZIF-8 MOF for RB4 which helps in water treatment [113]. They have carried out a docking study between ZIF-8 MOF (receptor) and RB4 (ligand) using AutoDock Vina to understand the absorption process computationally and the docking result is shown in Fig. 14. The net binding energy was found to be a negative value (− 22.34 kcal/mol) which means the molecular interaction is an exothermic adsorption process. The favorable binding interactions were due to ten H-bonding having a bond length ranging from 1.87 to 2.8 Å between oxygen atom (O) of –SO3 group in RB4 and hydrogen atoms (H) of –CH3 group in ZIF-8 MOF and three π–π interactions having bond length 4.78, 5.2, and 5.8 Å.Fig. 14Docked complex structure of zeolitic imidazole framework-8 (ZIF-8), a special class of metal organic framework (MOF) with organic molecule reactive blue-4 (RB4) ions using docking study with AutoDock Vina software [55, 95, 113]. ZIF-8 (receptor) and RB4 (ligand) are represented in stick and ball-and-stick models, respectively. H-bonds are represented with green and π–π interactions are shown with red dashed lines in the active site of ZIF-8 [113]. (Color figure online)Full size imageLu et al. in their work have used the molecular docking method using AutoDock 4 tool to investigate the

His co-workers have implemented molecular docking using AutoDock 4.2 Suite with Lamarckian genetic algorithm (LGA) as shown in Fig. 16 and the predicted binding energy was found to be − 2.32 kcal/mol, that indicates a stable absorption because of potential interactions on the surface.Fig. 16Docked complex structure of UiO-66(Zr) metal organic framework (MOF) and chrysene (CRY), a toxic and hazardous polycyclic aromatic hydrocarbon (PAH) pollutant using AutoDock 4.2 [115]. UiO-66(Zr) MOF (receptor) and CRY (ligand) are shown in stick and ball-and-stick models, respectively. UiO-66(Zr) is marked in white, violet, and red color. Four benzene rings of CRY are marked in blue and light gray color [115]. (Color figure online)Full size imageThe calculate energy due to different types of interaction potentials, such as van der Waals, hydrogen bonding and desolvation was − 3.1 kcal/mol and electrostatic was 0.79 kcal/mol. CRY was found to show electrostatic interaction with Zr4+ ion of the MOF.To understand the cause of instant isotopic exchange reaction in silver nanoparticles cluster, Chakraborty et al. have carried out molecular docking study between two [Ag25(DMBT)18]− (DBMT for 2,4-dimethylbenzenethiol, which acts as a protecting ligand) clusters using AutoDock 4.2 with Lamarckian genetic algorithm [100, 116]. [Ag25(DMBT)18]− has been used both as receptor and ligand in the docking process. The binding energy was found to be − 23.7 kcal/mol. The docking result with least binding energy is shown in Fig. 17.Fig. 17Docked complex structure of two [Ag25(DMBT)18]− clusters using AutoDock 4.2 [100, 115]. Complex is shown in ball-and-stick model. Silver (Ag) and sulfur (S) atoms are shown in gray and yellow, respectively. C–H… π interactions are viewed in green dotted lines. Hydrogen (H) atoms and benzene rings associated with these interactions are viewed in red and blue, respectively. Other benzene rings not associated with these interactions are shown in green [116]. (Color figure online)Full size imageThe fluorescent cobalt oxide (CoO) umbelliferone nanoconjugate having anti-cancer activity can be used both as a drug and carrier. Ali et al. have conducted molecular docking studies applying the protein docking program, HEX 8.0.0 using Spherical Polar Fourier Correlations technique to find the binding interactions of the

Using AutoDock MGL Tools, AutoDock Vina, Pymol visualization tool, and LigPlot+ version V.2.2.4. Simulations were performed on human insulin 3i40 obtained from the protein databank and phloretin molecules were drawn using ACD ChemSketch 2019.1.2.ConclusionsUV/Vis spectra showed that the interaction between PHL and INS produced strong absorption at a wavelength of 282 nm. The chromophore group of the aromatic amino acid ring has an absorption overlap with the PHL chromophore group. PHL and INS interactions occur at lower wavelengths with higher energies (blue shift and hyperchromic). The fluorescence analysis results showed that the excitation and emission occurred at a wavelength of 280 nm and 305 nm. Temperature changes did not affect INS emissions. However, the interactions of PHL and INS caused a 305–317-nm redshift. Temperature affected the binding constant (Ka) and the binding site (n). Ka decreased with increasing temperature and vice versa, but the binding site value increased. An indication that the stability of PHL and INS interactions is temperature dependent. The thermodynamic parameters such as enthalpy (ΔH0) and entropy (ΔS0) each have a value of − 16,514 kJ/mol and 22.65 J/mol·K. PHL and INS interaction formed hydrogen bonds and were hydrophobic. The free energy (ΔG0) values at all temperatures (288 K, 298 K, and 308 K) were − 23.04, − 23.26, and − 23.49 kJ/mol, respectively. PHL and INS interactions took place spontaneously. The quenching effect was dynamic and static. KD values (1.18 × 106, 1.13 × 106, and 1.12 × 106 M-1) were greater than those of KS (1.64 × 104, 1.62 × 104, and 1.60 × 104 M-1). The higher the temperature, the less KD and KS. The appearance of two negative signals on circular dichroism (CD) spectropolarimeter indicates the α-helix structure. The addition of PHL has revealed the proportion of α-helix in the insulin structure. PHL could stabilize the structure of insulin, indicating that phloretin induced regional configuration changes in insulin. Phloretin and insulin interacted and formed a complex. Furthermore, the stabilization of phloretin and enhancement of the α-helix structural configuration in insulin could be related to the phenomenon that phloretin can improve insulin resistance. Availability