Computational protocol: Molecular docking, a tool to determine interaction of CuO and TiO2 nanoparticles with human serum albumin

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Protocol publication

[…] Molecular docking studies were carried out using AutoDock 4.2 tool to predict the preferred binding mode and binding sites of TiO2 and CuO with HSA. The structure of TiO2 and CuO was drawn using ACD/ChemSketch and its geometry was optimized by combine use of Gaussian 03 program and Autodock 4.2. The crystal structure of HSA (PDB ID: 1E7I) was obtained from Protein Data Bank . Before docking analysis Hetatm were removed from the protein and the energy was minimized by SPDBV-Swiss-pdbviewer. For docking calculations, Lamarckian genetic algorithms (LGA) were used and grid parameters were set as 126×126×126, with a spacing of 1 Å, in AutoDock 4.2. To determine the preferred binding sites on HSA, TiO2 and CuO molecules were allowed to move within the whole region of HSA via 50 runs to obtain the possible binding gesture. The output from AutoDock was further analyzed with PyMOL and UCSF Chimera software package , . […]

Pipeline specifications

Software tools AutoDock, ChemSketch, Swiss-PdbViewer, PyMOL, UCSF Chimera
Applications Drug design, Protein interaction analysis
Chemicals Hydrogen