Import both ligand and receptor in maestro working panel • Select Glide - Receptor grid generation in the applications

pull down menu. • At first receptor protein should be imported then disable replace work space, fit to the screen and then import ligand into the workspace. • Click receptor tab in the panel and click the ligand in the work space. Green markers displayed on the ligand part. Now make sure that maestro has both ligand and receptor.

Pick the ligand manually – selects entry and click on ligand (ligand shows difference that it is selected) Click site tab. The enclosing box is shown in purple. Click centroid of selected residues (Note: for this you should know the active site residues) Specify residues manually by picking the residues or by selecting the residues (selecting the residues will be good) Go to sequence in selection box --- select your active sites amino acids and click add.

Nik

Click select residues button and choose active site residues of the protein or just click previous it will automatically accept the previous residues which we given as active site. • In constraints tab. click positional tab. Thus the sphere changes to yellow.Now click ok and see the pink color grid box found on receptor around your binding pocket.0 in the radius text box and click ok. • Then enter 2. Nik . Click new. thus new position dialogue box dialogue box opens. The gray sphere appears.

Nik . • Manually with cursor pick your active site residues. • The output file of the generated grid was in *. in that specify the working directory and file for storing output.zip format. • Then start the job by clicking start button. ( it will help for flexible movement of active site residues to dock in good interaction level) • Amino acids selected will be shown star as it is selected.Now go to Hbond Metal tab.

in that select the generated grid which was present in *. Nik . Glide runs Finish…….Ligand docking ---------Select Ligand docking in the glide module. • In the Ligand Docking panel. click the browse button in the receptor grid. • Leave other default options as such.mae format and it shows the glide score for docked ligand and receptor. browse and choose the minimized structure of the ligand which prepared in lig prep. • A file selector opens. • In the ligand docking-start panel we can specify the number of subjobs. Out put -- Select pose viewer file • Then start the docking job. • Glide results were visualized in interaction with protein and thereby Glide score was identified • Its output file was generated in glide_pv. ensure that precission option is standard precision or XP or HTVS HTLS – Speed but not accurate SP and XP– Accurate but Time taken (XP will give good score). For more rapid screening we can use HTVS option also. • In the docking section. • This is the best choice for Docking large number of ligands. • In the Ligand tab.out.zip format. which is present in the applications pull Down menu.

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