Computational protocol: Per-residue energy decomposition pharmacophore model to enhance virtual screening in drug discovery: a study for identification of reverse transcriptase inhibitors as potential anti-HIV agents

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Protocol publication

[…] The crystal structure of HIV-1 RT-GSK952 complex was obtained from PDB (2YNI). The steepest decent method and MMFF94S force field in Avogadro software were used to minimize conformation of HIV-1 RT-GSK952 complex. The crystal structure was opened on UCSF chimera to delete chain B and solvents (H2O, MG [magnesium atoms] and TAR [tartaric acid]). GSK952 was selected and deleted. GSK952 was prepared by adding hydrogen. The ligand was prepared using Antechamber and tLeap of Amber14 to optimize both HIV-1 RT (enzyme) and GSK952 (ligand), respectively, to ensure all parameters are present for MD simulations. Topology files generated were submitted for MD simulation. [...] AutoDock Vina was used for docking calculation. Geister partial charges were allocated during docking. AutoDock Graphical user interface provided by MGL tools were used to outline the AutoDock atom types. The docked conformations were obtained using the Lamarckian genetic algorithm. The magnitude of the grid box was x =14 Å, y =14 Å, z =18 Å, enclosing the anticipated active site residues including the highest contributing Leu100, Lys102, Lys103, Val106, Try188, and Phe227 residues. The classification of the compounds was in accordance with their docking score (DS) in a descending order. […]

Pipeline specifications

Software tools Avogadro, UCSF Chimera, AMBER, AutoDock Vina
Applications Drug design, Protein interaction analysis
Organisms Human immunodeficiency virus 2
Diseases Genetic Diseases, Inborn
Chemicals Amino Acids