Structural insights into conformational stability and binding of thiazolo-[2,3-b] quinazolinone derivatives with EGFR-TKD and in-vitro study

Identification of natural Rutaecarpine as a potent tobacco mosaic virus (TMV) helicase candidate for managing intractable plant viral diseases

“…The system usually reaches the equilibrium state after a series of dynamic simulations, and the post‐equilibrium trajectories are then analyzed to obtain a large amount of kinetic data to predict substance macroscopic properties. As a result, MDs has been widely appreciated and applied in designing biologically active molecules and studying ligand–receptor binding modes 32–35 . To evaluate the docked complexes stability, flexibility, compactness, and hydrophobic properties in their real‐time surroundings, the optimal conformation file of ligand–receptor binding (Autodock Vina 1.2.1) was used for MD simulation (Fig.…”

“…MM‐GBSA calculation was performed by using the g_mmpbsa module. The Gibbs free energy landscape (FEL) of protein–ligand was identified from protein systems (Gyrate and RMSD) using the gmx_sham module 33–35 …”

“…The Gibbs free energy landscape (FEL) of protein-ligand was identified from protein systems (Gyrate and RMSD) using the gmx_sham module. [33][34][35]…”

“…As a result, MDs has been widely appreciated and applied in designing biologically active molecules and studying ligand-receptor binding modes. [32][33][34][35] To evaluate the docked complexes stability, flexibility, compactness, and hydrophobic properties in their real-time surroundings, the optimal conformation file of ligand-receptor binding (Autodock Vina 1.2.1) was used for MD simulation (Fig. 9).…”

An exploration of the binding prediction of anatoxin-a and atropine to acetylcholinesterase enzyme using multi-level computer simulations

“…The molecular operating environment (MOE) software was used to perform the molecular docking [19,20] Following the docking methods first the protein was prepared by adding missing hydrogen using the Protnate-3D application and removed water molecules present in the x-crystallographic structure. Next, partial charges were assigned to the protein, and minimizations were carried out using the default force field (MMFF94x) [21][22][23]. The binding site was identified by employing Argus Lab 4.0.1 [24] and PrankWeb http://prankweb.cz/ [25] and following amino acids present in the binding site are A_120, A_121, A_122, A_124, A_125, A_126, A_130, A_133, A_202, A_203, A_286, A_287, A_293, A_294, A_295, A_296, A_297, A_337, A_338, A_341, A_447, A_448, A_72, A_74, A_75, A_83, A_86, A_87.…”