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.

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

Scripts to run Cross Docking in batch mode are found at:

    https://github.com/rizzolab/Benchmarking_and_Validation

This tutorial rebuilds systems in an aligned frame. Thus standard test set files are not applicable because proteins families will not necessarily be aligned at protein backbone. Instead of directly using a finalized and prepared test set as Pose Reproduction does, this prepares files from initial preparatory files. The list of necessary files are:

    ${pdb_id}.lig.moe.mol2
    ${pdb_id}.cof.moe.mol2 (if applicable)
    ${pdb_id}.rec.foramber.pdb

For further explanation of these 3 files see section "Preliminary File Preparation":

   https://ringo.ams.stonybrook.edu/index.php/Test_Set_Tutorial_V1

III.Preparing protein families

Enter CrossDocking Directory:

    cd Benchmarking_and_Validation/CrossDocking/

Protein families are a set of structures of the same protein in different conditions. This tutorial will not cover how protein families are determined, although one option is to restrict a family to structures with a single "UniProt ID" and no differing mutations within an active site. Lists of protein families can be found at (Note: see each paper for how families were determined):

    https://ringo.ams.stonybrook.edu/index.php/Rizzo_Lab_Downloads

A list of PDB codes for each protein family needs to be provided:

    cd zzz.family_lists

For each protein family, create a file with the name of the protein family, and list all PDB structures for that family:

    vi Acetylcholinesterase.txt

The file should like this (Note: The first PDB listed will be the reference which all other proteins are aligned to - a criteria should be chosen for which is first):

    1EVE
    1GPK
    1GPN
    ... 

After creating a file listing PDB codes for each protein family, create a file listing protein family names:

    vi zzz.Families.txt 

The file should look like this:

    Acetylcholinesterase
    ...

IV.Aligning protein families

The first step is to align protein families using the program UCSF Chimera along the backbone. This is done using the "mmaker" command and aligning all proteins to a single reference. The co-crystal ligand in each structure undergoes the same transformation alignment. (If Chimera is not available as a module this can be done in the gui.)

    module load chimera/1.13.1 

Certain variables need to be sourced every time a new session is started to run these scripts:

    source 000.source.env.sh

Edit slurm header and set path to testset (Same testset for Pose Reproduction which should have zzz.master as a subdirectory):

    vi 001.align.submit.sh

    sbatch 001.align.submit.sh

• • • Pic of aligned structs ***
    • Info about alignment

VI.Cross Docking Analysis

-SEE README FILE IN GIT REPO FOR ADDTIONAL DETAILS THAT MAY NOT BE COVERED HERE

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

Tutorial Written By: Christopher Corbo, Rizzo Lab, Stony Brook University (2024)

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>