2022 Denovo tutorial 3 with PDBID 1X70

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)