Cross Docking SB2024 V1 DOCK6.10 A
Under Construction
The purpose of this tutorial is to develop a uniform method to test cross docking across the Rizzo lab with the DOCK software. Note any data in this tutorial is solely for the purpose of example.
Contents
I.Introduction
- Cross docking is a test which is fundamentally similar to Pose Reproduction. If you are not experienced running Pose Reproduction yet, begin with:
https://ringo.ams.stonybrook.edu/index.php/Pose_Reproduction_Tutorial
- Cross docking measures pose reproduction accuracy with differing protein conformations/ structures as an additonal variable. It is a more translatable test to "real world" virtual screening, because it tests the ability to identify native poses, even when protein conformation/ sidechain packing is not induced to the particular ligand. When virual screening with a rigid receptor, the particular conformation chosen will not be ideal for all binder chemotypes, but it is desirable to predict near native poses in despite this.
II.Necessary files
III.Aligning protein families
IV.Docking molecules
V.Cross Docking Analysis
-SEE README FILE IN GIT REPO FOR ADDTIONAL DETAILS THAT MAY NOT BE COVERED HERE
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>>>>>>>>>>> Tutorial Written By: Christopher Corbo <<<<<<<<<<<<
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