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Molecular docking

LG Ling Guo
QY Qiang Yang
RW Runxiu Wei
WZ Wenjun Zhang
NY Na Yin
YC Yuling Chen
CX Chao Xu
CL Changrui Li
RC Randy P. Carney
YL Yuanpei Li
MF Min Feng
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Molecular docking analysis was performed to study the interaction between GTN and albumin. The 2D structure of GTN was generated by ChemDraw, then converted to 3D structure using Maestro LigPrep in OPLS3 force field, version 2.1.207. The X-ray structure of bovine serum albumin (PDB code: 4JK4) was obtained from the Protein Data Bank (http://www.rcsb.org/pdb). The Grid files were obtained following the standard procedure recommended by Schrödinger. The 3D structure of ligand was docked flexibly using Glide in XP mode, and other docking parameters were set to default values. Ten predicted poses were obtained during the docking process, and the docking score was calculated for each pose. The image files were generated by PyMOL (Version 1.7).

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