What is the most simple protocol to prepare the liberary of ligands for molocular docking ?

As a beginner in molecular docking, using iGEMDOCK or SwissDock can be a good starting point, as they are user-friendly and provide graphical interfaces. AutoDock Vina is another popular choice, but it requires more manual preparation steps and uses a command-line interface.

You can do as follow:

Obtain the ligand structures: First, you need to obtain the 3D structures of the ligands you are interested in. Common sources for ligand structures include the ZINC database (http://zinc.docking.org/) or PubChem (https://pubchem.ncbi.nlm.nih.gov/). You can download the ligand structures in a format compatible with your docking software, such as SDF or MOL2.

Convert the ligand file format: If needed, convert the ligand files to a format compatible with your docking software. For instance, AutoDock Vina and iGEMDOCK require PDBQT format, while SwissDock typically uses MOL2 format. You can use Open Babel (http://openbabel.org/) or similar software to perform the conversion.

Prepare the ligands: Ligand preparation involves adding hydrogens, assigning partial charges, and generating multiple conformations if necessary. For AutoDock Vina, you can use AutoDockTools (ADT) or MGLTools (https://ccsb.scripps.edu/mgltools/) to prepare the ligands in PDBQT format. For SwissDock, you can use the Swiss-PdbViewer (http://spdbv.vital-it.ch/) or Chimera (https://www.cgl.ucsf.edu/chimera/) to prepare the ligands in MOL2 format. For iGEMDOCK, the software itself can prepare ligands in the required format.

Create a ligand library: Compile all prepared ligands into a single directory or file, depending on your docking software's requirements. This will allow you to load them as a batch for docking.

Prepare the protein: Obtain the 3D structure of the protein target, usually from the Protein Data Bank (https://www.rcsb.org/). Clean the structure by removing water molecules, adding hydrogens, and assigning charges. Define the docking site or grid box for your docking calculations.

Perform docking: Load the prepared protein structure and ligand library into your docking software, and perform the docking calculations. The software will generate docking poses and provide scores to rank the ligands based on their predicted binding affinities.

Please find the following video tutorials on youtube: https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwihpPTituD-AhXAbKQEHV_ZB9YQtwJ6BAgHEAI&url=https%3A%2F%2Fwww.youtube.com%2Fwatch%3Fv%3DRHvEVArxpas&usg=AOvVaw2vAeA_z-oIOzzPSxRH0TF6 ------- https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwihpPTituD-AhXAbKQEHV_ZB9YQtwJ6BAgnEAI&url=https%3A%2F%2Fwww.youtube.com%2Fwatch%3Fv%3DMX6MQL8Evjo&usg=AOvVaw3Ctu20e48KkNyir42YxpKc

Kaushik Sarkar

The most simple protocol to prepare a library of ligands for molecular docking typically involves the following steps:

Obtain ligand structures: Collect the structures of the ligands you wish to dock. These structures can be obtained from public databases, literature, or synthesized. Example: Public Database such as ZINC15 or PubChem.

Clean up the structures: Ensure that the ligand structures are free from any errors or inconsistencies.

Generate 3D conformers: Generate multiple 3D conformations of each ligand using a conformer generation tool such as ACD lab ChemSletch or Chemdraw. This step is important to account for ligand flexibility during the docking process.

Minimized energy structure: All ligand structures must be energatically minimized by semiempirical (MMFF94 force field of Avogadro) or quantum chemical (DFT by Gaussian software) method.

Choose receptor: You must require a suitable target (receptor) from your knowledge. The 3D crystal structure of the receptor is come from PDB server.

Prepare the receptor: You must require to delete waters and other co-crystalized ligand from the receptor. Then prepare the receptor structure by adding missing atoms, assigning charges. This step can be done using software tools such as AutoDock Tools.

Dock the ligands: Finally, use a molecular docking program such as AutoDock, to dock the ligands to the receptor.

It is important to note that while this protocol is simple, it may not be sufficient for more complex docking studies. Depending on the research question, additional steps such as ligand alignment or binding site identification may be necessary.

Here, I have attached some information links of related softwares:

ZINC Database: https://zinc15.docking.org/

ACD ChemSketch: https://www.acdlabs.com/resources/free-chemistry-software-apps/chemsketch-freeware/

ChemDraw: https://perkinelmerinformatics.com/products/research/chemdraw

PubChem Database: https://pubchem.ncbi.nlm.nih.gov/

Avogadro: https://avogadro.cc/

Protein Data Bank: https://www.rcsb.org/

Auto Dock Tools (for docking): https://ccsb.scripps.edu/mgltools/downloads/

OpenBabel (for changing ligand format): http://openbabel.org/wiki/Main_Page

PymoL (Docking result visualize): https://pymol.org/2/

Discovery Studio (Docking result visualize): https://discover.3ds.com/discovery-studio-visualizer-download

Molecular Docking Tutorial:

1. One ligand docking: https://www.youtube.com/watch?v=k6tqCeDIwEk

2. Multiple ligand docking: https://www.youtube.com/watch?v=tFFxNTvvoJI

Hello fellow researcher .. What is the meaning of your name?

Can we classify HV and LV lines based on line length?

Is There Any Feasible Method To Test Fluorescent Compounds Other Than Fluorescence Spectrometers ??

What is the characteristic length to determine the Reynolds number for the scattered turbulent fluid flow?

I am interested in medicinal chemistry field, which books are highly recommended to learn from?

Could you please recommend some good journal that accept very long revie papers (approximately 6000+ words) in neurosurgery, cancer biology ?

Does anyone have kinetic and kinematic dataset for gait classification?

How to assign different material properties to each element in Abaqus ?

How to choose ANN number of hidden layers and nodes?

Which is better medicine or food in obesity?

What are the potential shell well and atomic solvation parameters for the boron atom?

How to Remove different version of atom from pdb Crystal Structure for Docking Preparation?

The dimensionality of protein and ligand is reduced after docking?

How to generate .dlg files on PyRx?

Servers for finding free energy and dissociation constant of protein-protein docked complex?

What would be the best option to dock a number of peptides to a protein?

Could one suggest a common formula for Penicillium Chrysogenum spore counting by spectroscopy? and also its nm?

Why train curves are being repeated in this five fold cross validation?

Is there any online webserver for DNA-ligand docking?

I am looking to learn docking studies online can any one help?