Difference between revisions of "Pose Reproduction 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 pose reproduction across the Rizzo lab with the DOCK software. Note any data in this tutorial is solely for the purpose of example.

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, Rizzo Lab, Stony Brook University (2024)

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