Difference between revisions of "Cross Docking SB2024 V1 DOCK6.10 A"
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==I.Introduction== | ==I.Introduction== | ||
| − | - Cross docking is a test which is fundamentally similar to | + | - 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 | 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. | - 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. | ||
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| + | - 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== | ==II.Necessary files== | ||
Revision as of 22:50, 27 January 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.
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 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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