Molecular docking runs were performed using the AutoDock4.0 program [47 (link)]. The AutoDock tools suite was used to prepare the proteins and ligands. During the preparation, polar hydrogens were incorporated into the rLiD1 and rHNC models, and Kollman United atom charges and atomic salvation parameters were assigned. SM and LPC structures were extracted from the Pub chem database [48 (link)], and Gasteiger atomic charges were appointed.
Electron affinity and electrostatic potential were calculated with the Autogrid program [47 (link)]. The grid map comprised 85 × 100 × 120 points, with a grid spacing of 0.375 Åusing distance-dependent dielectric constants. Molecular docking was performed using 200 runs of the GA-LS method with a maximum number of energy evaluations of 27,000,000 for each run. After docking, all the generated structures were assigned to clusters based on a tolerance of 2.0Åall-atom root-mean-square deviation (RMSD) from the lowest-energy structure. Specific interactions between the proteins and the possible binding modes were analyzed using UCSF Chimera [49 (link)] and Discovery Studio Visualizer [50 ].
Electron affinity and electrostatic potential were calculated with the Autogrid program [47 (link)]. The grid map comprised 85 × 100 × 120 points, with a grid spacing of 0.375 Åusing distance-dependent dielectric constants. Molecular docking was performed using 200 runs of the GA-LS method with a maximum number of energy evaluations of 27,000,000 for each run. After docking, all the generated structures were assigned to clusters based on a tolerance of 2.0Åall-atom root-mean-square deviation (RMSD) from the lowest-energy structure. Specific interactions between the proteins and the possible binding modes were analyzed using UCSF Chimera [49 (link)] and Discovery Studio Visualizer [50 ].
Free full text: Click here
