2022 Denovo tutorial 3 with PDBID 1X70

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Revision as of 12:07, 20 March 2022 by BrockBoysan (talk | contribs) (System Preparation)
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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 each of the fragment libraries

All of the linkers from fraglib_linker.mol2, fragments with 2 non-Hydrogen rotatable bonds in 715

All of the sidechains from fraglib_linker.mol2, fragments with 1 non-Hydrogen rotatable bonds in 715