Im running molecular docking on insulin and a DNA sequence, but the insulin is having to many torsions (140 active torsion but the maximum torsion allowed is only 32 with autodock vina). Eventhough exceeded the maximum torsion, the docking still can be run but the issue is its impact on the outcome. Is it ok to ignore the torsion issues while running molecular docking? if not, how should I identity the unwanted torsions? Please send help, I have no idea on this.
I think Autodock vina is not suitable enough to handle molecules like peptides. I suggest switching to docking servers like HADDOCK (https://rascar.science.uu.nl/haddock2.4/), ClusPro (https://cluspro.bu.edu/login.php), or ROSETTA (https://rosie.rosettacommons.org/docking/). If you absolutely have to use Autodock, they have this module for peptides called Crankpep (https://ccsb.scripps.edu/adcp/) which may help, although it might also have some limitations.
Chong Qi I don't have a definite answer, but HADDOCK and ROSETTA should be good enough.
it typically means the ligand you're working with has too many rotatable bonds (torsions), which increases conformational flexibility and computational complexity. Most docking tools like AutoDock, AutoDock Vina, or others often set a limit—commonly 32 torsions.
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