Difference between revisions of "Cross Docking SB2024 V1 DOCK6.10 A"

Revision as of 19:35, 13 February 2024

!!!!!!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.

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 nonetheless it is desirable to predict near native poses.

- The outcomes for cross docking are the same as pose reproduction, although there is a fourth outcome termed "incompatible". This is when a ligand is energetically incompatible in its native pose when complexed in an alternative, rigid, structure of the protein.

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, Rizzo Lab, Stony Brook University (2024)

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