Difference between revisions of "Pose Reproduction SB2024 V1 DOCK6.10 A"
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==I.Introduction== | ==I.Introduction== | ||
| + | -Pose reproduction is an experiment which tests a docking programs ability to predict the bound pose of a ligand to a receptor (typically a protein). | ||
| + | An experimental structure of a protein-ligand complex is converted into 2 separate files, 1 for ligand and 1 for receptor. The docking program then predicts the binding orientation that is most energetically favorable. In the case of DOCK6, the ligand is flexibly docked with the Anchor & Grow algorithm to a rigid receptor. | ||
| + | |||
| + | -The RMSD between the docked poses and experimental pose are measured. We consider RMSD < 2 angstroms an accurate prediction. There are 3 outcomes we classify. | ||
| + | 1) Success - The best scoring pose is < 2 angstroms | ||
| + | 2) Scoring Fail - A pose < 2 angstroms was sampled but did not score best | ||
| + | 3) Sampling Fail - No pose < 2 angstroms was sampled | ||
==II.Necessary files== | ==II.Necessary files== | ||
Revision as of 02:08, 25 January 2024
Under Construction
The purpose of this tutorial is to develop a uniform method to test pose reproduction across the Rizzo lab with the DOCK software. Note any data in this tutorial is solely for the purpose of example.
Contents
I.Introduction
-Pose reproduction is an experiment which tests a docking programs ability to predict the bound pose of a ligand to a receptor (typically a protein). An experimental structure of a protein-ligand complex is converted into 2 separate files, 1 for ligand and 1 for receptor. The docking program then predicts the binding orientation that is most energetically favorable. In the case of DOCK6, the ligand is flexibly docked with the Anchor & Grow algorithm to a rigid receptor.
-The RMSD between the docked poses and experimental pose are measured. We consider RMSD < 2 angstroms an accurate prediction. There are 3 outcomes we classify. 1) Success - The best scoring pose is < 2 angstroms 2) Scoring Fail - A pose < 2 angstroms was sampled but did not score best 3) Sampling Fail - No pose < 2 angstroms was sampled
II.Necessary files
III.Docking molecules
IV.Pose Reproduction 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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