How to dock my ligand with a cofactor NADPH in AutoDock?

use PyRx free software and east yo use.

PyRx is a graphical user interface for AutoDock, making molecular docking more accessible through a user-friendly interface. Here's how you can dock a ligand with a cofactor like NADPH using PyRx:

Prepare Ligand and Cofactor Structures:Obtain the 3D structures of your ligand and NADPH in a compatible format such as PDB or mol2.

Launch PyRx:Start PyRx on your computer. Ensure that you have AutoDock installed and configured with PyRx.

Import Receptor and Ligand Structures:Go to "File" > "Import Molecule(s)" to load your receptor protein structure (receptor.pdb) and ligand structure (ligand.pdb/mol2) into PyRx.

Prepare the Receptor:Define the binding site on the receptor where you want the ligand to dock. You can select the binding site manually or by using PyRx's built-in tools for defining the grid box.

Prepare the Ligand:Select the ligand molecule in the PyRx workspace. Assign rotatable bonds to the ligand if needed, using PyRx's tools for adjusting ligand flexibility.

Set Docking Parameters:Configure the docking parameters in PyRx, including the search space, grid spacing, and number of runs. You can adjust these parameters based on your specific requirements and the characteristics of your system.

Run Docking Calculation:Initiate the docking calculation by clicking on the "Run AutoDock" button or a similar option in PyRx. PyRx will perform the docking simulation using AutoDock, exploring different ligand conformations and orientations within the receptor binding site.

Analyze Docking Results:Once the docking calculation completes, analyze the results using PyRx's visualization tools. PyRx allows you to visualize and compare the docked ligand conformations, as well as assess the binding affinity and interaction energies.

Refinement and Optimization (Optional):If necessary, refine and optimize the docking results by adjusting parameters, re-running docking simulations, or performing post-docking analysis using PyRx.

Save Results:Save the docking results and any relevant data or analysis for further study and interpretation.

By following these steps in PyRx, you should be able to perform molecular docking of your ligand with the NADPH cofactor efficiently and effectively. Make sure to refer to PyRx's documentation and tutorials for additional guidance and best practices specific to the software.

Jobin Thomas

There are a lot of tutorials in youtube.... You can easily follow those..

Regards

Muzammil Kabier

https://sourceforge.net/projects/mzdock/ you can use this app MzDOCK which has the capability to restore your cofactors/ions while docking.

Alfaris Muammar

Ankit Negi but it is possible if I use autodocktools or it can’t ?

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