Author: Pervushin, Konstantin; Tan, Edward; Parthasarathy, Krupakar; Lin, Xin; Jiang, Feng Li; Yu, Dejie; Vararattanavech, Ardcharaporn; Soong, Tuck Wah; Liu, Ding Xiang; Torres, Jaume
Title: Structure and Inhibition of the SARS Coronavirus Envelope Protein Ion Channel Document date: 2009_7_10
ID: 1e102wrc_59
Snippet: According to the chemical shift changes observed after addition of HMA, two ETM pentameric models were obtained. For one model, residues 8-12 and 17-38 did not change after exposure to HMA. For the second model, residues 8-30 did not change. Docking of HMA to these two models was performed using Glide [68, 69] with standard parameters, guided by NOE constraints, and allowing for HMA flexibility. The binding site was defined in terms of two concen.....
Document: According to the chemical shift changes observed after addition of HMA, two ETM pentameric models were obtained. For one model, residues 8-12 and 17-38 did not change after exposure to HMA. For the second model, residues 8-30 did not change. Docking of HMA to these two models was performed using Glide [68, 69] with standard parameters, guided by NOE constraints, and allowing for HMA flexibility. The binding site was defined in terms of two concentric cubes: the bounding box, which contains the center of any acceptable ligand pose, and the enclosing box, which contains all ligand atoms of an acceptable pose. Upon completion of each docking calculation, the best docked structure was chosen using a Glidescore (Gscore) function, a modified and extended version of the empirically based Chemscore function.
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