Autodock Vina Tutorial | Grid Box Generation

Рет қаралды 4,953

Күн бұрын

AutoDock Vina requires pre-calculated grid maps, one for each atom type present in the ligand being docked. This helps to make the docking calculations fast. A grid map consists of a three-dimensional lattice of regularly spaced points, sur- rounding (either entirely or partly), and centered on some region of interest of the macromolecule under study. This could be a protein, enzyme, antibody, DNA, RNA, or even a polymer or ionic crystal. Typical grid point spacing varies from 0.2Å to 1.0Å, and the default is 0.375Å (roughly a quarter of the length of a carbon-carbon single bond). Each point within the grid map stores the potential energy of a ‘probe’ atom or functional group that is due to all the atoms in the macromolecule.

Пікірлер: 29

@user-yo3tm7jf4m 11 ай бұрын

Sir, I have docked a protein and ligand using Autodock Vina and visualized using Biovia Discovery Studio. I have two doubts. (1) Should I be bothered if the Kollman and Gasteiger charges added are not in the range of -1 to +1? (2) When visualizing the docked products in Biovia, sometimes one or two unfavorable bonds are showing in red colour. Should I be bothered about this? Please help me.

@BioinfoCopilot 11 ай бұрын

You should consider each and every parameters before publishing. The charges you mentioned depends on the charge of the protein and the ligand respectively. Choose conformations which ever has the best parameters. Its not mandatory to choose the best conformations only as the values or the binding energies obtained are absolute values. If you want to try the best conformation then do molecular dynamics simulation to understand the structure more precisely.

@rohitchel5679 4 ай бұрын

Im performing docking on a known active site so i limited the gridbox around the active site only. Some of the conformations i got after docking were outside the grid box. Is that normal?

@BioinfoCopilot 4 ай бұрын

I have answered in other post

@lanai-wy4fr 6 ай бұрын

Hello sir, this is a very helpful video but I was wondering how do you get the AutoDock Structure File? Is it the bdpqt itself or something else? I would really appreciate your answer. Thank you for sharing this helpful information!

@BioinfoCopilot 6 ай бұрын

Thank you. I made another video regarding this kzbin.info/www/bejne/rWa6c599r86WqLMsi=24P059O1vM-SJmJG

@miow10 Жыл бұрын

Thank you for the tutorial. For targeted docking, if I have a few known active/binding site, I just select a few residue right? Then, for the grid box adjustment, I need to ensure the box covered all the residues selected. But how do I choose on which residue should I set as the center of the grid box?

@BioinfoCopilot Жыл бұрын

Generally, for the targeted docking you set ~4-5 Angstrom regions or more if you have more residues. What you can do is open your structure file in UCSF chimera and select one of your active site residues and span upto 5 Angstrom. Then have a look whether all the residues are covered or not. Replicate the same in MGL tools.

@alptekin6299 4 ай бұрын

what are the requirements for targeted docking? when blind docking, how does it affect the accuracy? I am dealing with several pair of protein-ligands and some of them seem to have inhibitor ligands inside of them while some of them don't so I'm lost

@BioinfoCopilot 4 ай бұрын

The targeted docking works for already known ligand bound to proteins derived through X-ray crystallography. When you know the exact position of the ligand binding, then you perform targeted docking. You can perform both 1. First do blind docking to all and then those which have ligand bound check the results from blind docking and match it. If it matches, then your blind docking approach seems to work.

@shubhedu.science3638 4 ай бұрын

Hello sir.... Really very informative video. I just started to learn docking.... Want to learn this for research. Thank you. Dr.Shubhangi Patil. Institute of Science Mumbai.

@BioinfoCopilot 4 ай бұрын

I am glad that it helped. My pleasure 😇

@shubhedu.science3638 4 ай бұрын

Hello sir.... Is it enough to use free softwares for good publication or PhD research topic. I also go through your papers. Great work

@BioinfoCopilot 4 ай бұрын

@shubhedu.science3638 Yes absolutely. The world is heading towards open-source soon.

@shubhedu.science3638 4 ай бұрын

@@BioinfoCopilot Thank you

@boorasanjit2013 2 жыл бұрын

sir, please make video on molecular dynamics simulation

@ananyapandey2577 7 ай бұрын

Sir...i wanted to create a grod box around a protein but the grid box is not appearing whereas it is appearing for other IDs

@BioinfoCopilot 7 ай бұрын

The protein might be too big. Or explore the grid options.

@phuochuynh1777 10 ай бұрын

Thank you sir. One question, when i know active site, and setting grid box for active site. But the ligand docked was not fit into active site. How can i improve my docking?

@BioinfoCopilot 10 ай бұрын

Thank you. Setting the grid box by choosing exact residues will help. OR you can try to increase the no of poses to 200 or something.

@phuochuynh1777 10 ай бұрын

thank you sir. How can i set 200 of pose parameters?@@BioinfoCopilot

@rohitchel5679 4 ай бұрын

Im performing docking on a known active site so i limited the gridbox around the active site only. Some of the conformations i got after docking were outside the grid box. Is that normal?