Difference between revisions of "2025 DOCK tutorial 2 with PDBID 1XMU"

Revision as of 13:38, 7 March 2025

Introduction

Structure Preparation

The objectives of this section are:

1. Structural Evaluation

  a. Identify any missing loops in the protein structure
  b. Assess metal coordination atoms for key interactions with the protein

2. Protein Receptor Preparation

  a. Generate protein structure in mol2 format
  b. Add hydrogen atoms
  c. Assign appropriate charges
  d. Save the refined protein structure in mol2 format

3. Ligand Preparation

  a. Generate ligand structure in mol2 format
  b. Add hydrogen atoms
  c. Assign appropriate charges
  d. Save the refined ligand structure in mol2 format

4. Alternative method of protein and ligand preparation: Using Dock Prep

1. Structural Evaluation

a. Open the downloaded PDB structure in Chimera (In this tutorial, 1XMU). Check for missing loops—these appear as dashed lines in the structure. There are no missing loops in the structure 1XMU, so no further action is needed.

If you find missing loops in your structure, you will need to fix them before proceeding. Refer to (Tutorial 2025 [[1]]) for instructions on fixing missing loops.

b. In 1XMU, there is metal coordination atoms (Zinc and Magnesium) interacting with the protein. It is important to keep them intact and not delete them during protein preparation

2. Protein Receptor Preparation

a. Generate protein structure in MOL2 format

i. Open the downloaded pdb file (1XMU) in Chimera,

ii. Remove ligand: Go to Select → residue → ligand to highlight the ligand

iii. Then, go to Actions → Atoms/Bonds → Delete

iv. Repeat the process to delete water molecules by selecting HOH instead of ligand

v. Save the protein, Go to File → Save Mol2. 1XMU_Rec_nCH.mol2 ('no' Charge and Hydrogen)

b. Add Hydrogen atoms

i. Go to Tools → Structure Editing → AddH. A dialogue box like this will appear, adjust as needed

ii. Select OK to proceed. If successful, You will get a confirmation message 'Hydrogens Added'

c. Assign appropriate charges

i. Go to Tools → Structure Editing → Add Charge

A dialogue box like this will appear, adjust as needed. For this tutorial, we will use Gasteiger charges. Leave all other settings as they are, then click OK.

ii. A new pop-up menu will appear

iii. Just as before, make sure that Gasteiger is selected. All other defaults are okay.

iv. Select OK. If successful, You will get a confirmation message 'standard charges added'

d. Go to File → Save Mol2. 1XMU_Rec_wCH.mol2 ('with' Charge and Hydrogen)

3. Ligand Preparation

a. Generate ligand structure in mol2 format

i. Open the downloaded pdb file (1XMU) in Chimera,

ii. Remove protein: Go to Select → residue → ligand to highlight the ligand

iii. Then, go to Select → Invert (selected models)to select everything except the ligand

iv. Go to Actions → Atoms/Bonds → Delete

iv. Save the ligand, Go to File → Save Mol2. 1XMU_lig_nCH.mol2 ('no' Charge and Hydrogen)

b. Add Hydrogen atoms

i. Go to Tools → Structure Editing → AddH

ii. The next menu will be the same as when adding hydrogens during receptor preparation. Use the same settings as before

c. Assign appropriate charges

i. Go to Tools → Structure Editing → Add Charge

ii. The next menu will be the same as when adding hydrogens during receptor preparation. Use the same settings as before

Emphasis: For this tutorial, we will use Gasteiger charge

d. Go to File → Save Mol2. 1XMU_lig_wCH.mol2 ('with' Charge and Hydrogen)

4. Alternative Method for Protein and Ligand Preparation: Using Dock Prep

This method simplifies preparation by adding hydrogens and assigning charges in a single step.

i. Open the PDB file (1XMU) in Chimera

ii. Isolate the protein and ligand following the steps in Sections 2a and 3a

iii. Go to Tools → Structure Editing → Dock Prep

iv. A pop-up menu will appear – leave all default parameters (as seen below) and click OK

v. The next set of drop-down menus will follow the same process as adding hydrogens and charges manually

vi. The final pop-up menu will be the Save MOL2 window

File:1xmu-dockprep menu.png

Grid Generation

Energy Minimization

Docking

Virtual Screening

Cartesian Minimization

Rescoring and Ranking