I possess a natural compound with a size of 70,000. Can I perform docking using PyMOL in a reasonable amount of time? If feasible, what is the estimated duration for completion?
Dear Punet Kumar
PyMOL is primarily a molecular visualisation tool, and while it has some basic docking efficiency, it may not be the most efficient tool for high-throughput docking.
For large-scale docking studies, specially designed programs such as AutoDock, AutoDock Vina, or other molecular docking programs designed for efficiently handling a large number of molecules can be used.
Thanks
Satyendra
Hello,
For a calculation of this magnitude I recommend using software that allows execution via a terminal. In theory you can dock any number of compounds in a single run. In practice you have to take into account factors such as the support of your docking program or memory occupation (RAM primarily). As for the timing, they are highly variable and depend on: the hardware specifications of your machine, the docking program used, the chemical characteristics of the molecules to be docked and the parameters used to perform the calculation.
Hello Punet Kumar, As Satyendra Singh highlighted, PyMol primarily functions as a visualization tool and lacks inherent docking capabilities unless supplemented with extensions. If your goal is to conduct docking experiments involving multiple ligands with a single protein in a single run, I recommend considering AutodockVina. This software is both free and open-source, providing a robust solution for your docking needs.
Dear Punet Kumar ,
Yes, it is possible to perform a number of compounds to be included in the docking studies in a single run. As everyone highlighted before, you can use either free software such as Autodock-based programs, mainly Smina or Vina, or commercial software such as MOE or Glide.
Regarding practicality, both MOE and Glide are easier to use because they support GUI. However, if you are familiar with Terminal and scripting, and know how to execute commands, I suggest you use Autodock Vina or Smina for your research purposes.
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