Molecular Docking | Autodock VINA Virtual Screening | VINA Docking tutorial | Bioinformatics
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Published 2020-07-30
The Docking aims to predict the ligand-protein complex structure by exploring the conformational space of the ligands within the binding site of the protein. A scoring function is then utilized to calculate the free energy of binding between the protein and the ligand in each docking pose or confirmation. Docking and scoring produce ranked compounds, which are then post-processed by examining calculated binding scores, validity of generated pose, undesirable chemical moieties, metabolic liabilities, desired physicochemical properties, lead-likeness, and chemical diversity.
Post-processing results can filer down the compounds, which can be further proceed to experimental assay to identify potential compounds.
AutoDock Vina significantly improves the average accuracy of the binding mode predictions compared to AutoDock 4.
MGL Tools: mgltools.scripps.edu/
Autodock Vina: vina.scripps.edu/index.html
OpenBabel: bit.ly/3eMgXZm
Perl: padre.perlide.org/
PerlScript File: bit.ly/31gNgef
Literature:
www.nature.com/articles/s41598-018-23768-7
pubmed.ncbi.nlm.nih.gov/28809009/
experiments.springernature.com/articles/10.1007/97…
All Comments (21)
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You just saved my undergraduate thesis research. Thank you so much!!
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Thank you this has been VERY VERY helpful and I really appreciate your tutorial. Everything is so clear and I love how you also provided sources on where to find downloads :)
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Thank you! How do I add new atom types in Vina, specifically for Silicon? Is there a parameter file like GPF or DPF that needs to be edited?
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This video tutorial is truly helpful for my thesis. I have a question though... Why is the exhaustiveness parameter is not typed out in the configuration file or Vina will carry it out at default ?
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Thank you very much. It is an excellent tutorial for virtual screening in Autodock Vina
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It's an excellent tutorial for virtual screening using autodock vina
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Thank you so much for the video. I have a little question about the small peptide as ligands. when I transform it from pdb file into pdbqt file. it was broken (when i visualize them by chimera X or pymol). Do you have any solution for the transformation ?
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Thanks for your lectures Sir Can you please explain the steps of ( metal complex) docking??
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Thank you this was very informative and easy to follow. Much appreciated.
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Wonderful tutorial! This will save me a lot of time (8 protein targets and 23 ligands). I was going to be very selective about the ligands, but I don't have to be now.
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Great job, Thank you so much Professor.
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This is another master piece from you sir. Kindly add tutorials about ligand DNA docking using autodock. Thanks regards
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this tutorial is very helpful in my thesis!! i want to add it in citation. which journals can I cite?
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This was SO MUCH helpful!! Thank you for the amazing explanation!
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Thank you sir for this wonderful guidance !
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thank you for this, is this still the easiest way to use autodock vina for screening a library of ligands?
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Hello Sir I hope you are doing great I have tried to use the perl script with the new version of Vina (v 1.2.3) but Vina didn't recognize the --log argument in the script. Is there any problem/modification?
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Thank you so much, this is very informative and help me a lot in doing Autodock
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Youre amazing. Thank you so much.
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hey sir, why don't we just use Pyrx ? is there any difference with accuracy or sth else?
