P. 1
Glide Steps

Glide Steps

|Views: 39|Likes:
Publicado porselnikraj

More info:

Published by: selnikraj on Nov 26, 2010
Direitos Autorais:Attribution Non-commercial

Availability:

Read on Scribd mobile: iPhone, iPad and Android.
download as PDF, TXT or read online from Scribd
See more
See less

11/26/2010

pdf

text

original

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

Nik .0 in the radius text box and click ok. Click new. 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. The gray sphere appears. thus new position dialogue box dialogue box opens.Now click ok and see the pink color grid box found on receptor around your binding pocket. • In constraints tab. Thus the sphere changes to yellow. • Then enter 2. click positional tab.

zip format. • Manually with cursor pick your active site residues. in that specify the working directory and file for storing output. • 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. • The output file of the generated grid was in *. Nik .

• A file selector opens. • In the docking section. in that select the generated grid which was present in *. Out put -- Select pose viewer file • Then start the docking job. • In the ligand docking-start panel we can specify the number of subjobs.Ligand docking ---------Select Ligand docking in the glide module. • This is the best choice for Docking large number of ligands. Nik .zip format. browse and choose the minimized structure of the ligand which prepared in lig prep.out. 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). • In the Ligand tab. • In the Ligand Docking panel. • Leave other default options as such. For more rapid screening we can use HTVS option also. Glide runs Finish…….mae format and it shows the glide score for docked ligand and receptor. • Glide results were visualized in interaction with protein and thereby Glide score was identified • Its output file was generated in glide_pv. click the browse button in the receptor grid. which is present in the applications pull Down menu.

You're Reading a Free Preview

Descarregar
scribd
/*********** DO NOT ALTER ANYTHING BELOW THIS LINE ! ************/ var s_code=s.t();if(s_code)document.write(s_code)//-->