Difference between revisions of "2022 Denovo tutorial 3 with PDBID 1X70"

From Rizzo_Lab
Jump to: navigation, search
(System Preparation)
(System Preparation)
Line 14: Line 14:
 
Now load up Chimera:
 
Now load up Chimera:
  
   Tools > Binding/Surface Analysis > View Dock > Load each of the fragment libraries
+
   Tools > Binding/Surface Analysis > View Dock > Load fraglib_linker.mol2
  
  
Line 20: Line 20:
 
[[File:1X70_linkers.png|thumb|center|800px|All of the linkers from fraglib_linker.mol2, fragments with 2 non-Hydrogen rotatable bonds in 715]]
 
[[File:1X70_linkers.png|thumb|center|800px|All of the linkers from fraglib_linker.mol2, fragments with 2 non-Hydrogen rotatable bonds in 715]]
  
 +
  Load fraglib_sidechain.mol2
  
[[File:1X70_sidechains.png|thumb|center|800px|All of the sidechains from fraglib_linker.mol2, fragments with 1 non-Hydrogen rotatable bonds in 715]]
+
[[File:1X70_sidechains.png|thumb|center|800px|All of the sidechains from fraglib_sidechain.mol2, fragments with 1 non-Hydrogen rotatable bonds in 715]]
 +
 
 +
  Load both
  
 
[[File:715_frags.png|thumb|center|800px|All of the fragments from 715 loaded in (bottom, sea blue) and 715.mol2 (top) ]]
 
[[File:715_frags.png|thumb|center|800px|All of the fragments from 715 loaded in (bottom, sea blue) and 715.mol2 (top) ]]

Revision as of 12:19, 20 March 2022

System Preparation

Directory Setup

ATTENTION: This tutorial requires you to have first completed the 2022 1X70 VS tutorial: https://ringo.ams.stonybrook.edu/index.php/2022_DOCK_tutorial_3_with_PDBID_1X70

Make a new directory:

 mkdir 09.focus_dn

Now inside 09.focus_dn, make the following DOCK6 input file:


Now load up Chimera:

 Tools > Binding/Surface Analysis > View Dock > Load fraglib_linker.mol2


All of the linkers from fraglib_linker.mol2, fragments with 2 non-Hydrogen rotatable bonds in 715
 Load fraglib_sidechain.mol2
All of the sidechains from fraglib_sidechain.mol2, fragments with 1 non-Hydrogen rotatable bonds in 715
 Load both 
All of the fragments from 715 loaded in (bottom, sea blue) and 715.mol2 (top)