We have created a facebook group that aims to share experience on Molecular Docking experiments & Softwares.
As seen o Wikipedia "In the field of molecular modeling, docking is a method which predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex"
In this group you can share your opinions, your experience, bugs, questions or informations about all docking softwares and technologies.
If you are interested in docking please join us...
https://www.facebook.com/groups/1460292600663415/
https://www.facebook.com/groups/1460292600663415/
I think so. Because especially drug design experiments depends on docking. Also in our laboratory we are using this kind of experiments for simulating mutations, in-silico binding experiments etc. Of course if I am wrong please write me to correct sentences
I think that molecular docking calculation cannot be called "experiment". But I know some molecular modelers who defend molecular modeling by saying that molecular modeling calculations are experiments. Perhaps it is a subjective matter but . . .
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The protein and ligand molecules in molecular docking are not real entities. One cannot take a protease and cleave the protein or separate the ligand from the protein and administer that ligand to a laboratory animal or to a patient.
When one looks into a source code of any molecular modeling tool, it is a sea of abstract mathematical operations. It just does not go beyond math and out into the real world.
I use the word "calculation" for modeling of a state, "simulation" for modeling of a process, and "experiment" for the real thing.
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And even If drug design experiments depend on molecular docking (maybe; a little bit; sometimes) it does not automatically mean that a molecular docking calculation is an experiment, because then one could argue that one's commuting is an experiment because if one does not get to the lab one will not be able to do drug design experiments.
This is a subjective matter. Molecular docking is certainly a type of computer simulation and simulations are usually used to assist wet-lab experiments. But computer simulations can be termed as "computer experiments" as well ("in silico experiments"). Perhaps it is necessary to make a distinction between "physical" and "computer" experiments here.
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