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Selecting Water molecules and hetetoatims
https://www.dockingserver.com/forum/viewtopic.php?f=2&t=57
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Author:  iftahG [ Mon Jul 18, 2011 7:03 pm ]
Post subject:  Selecting Water molecules and hetetoatims

In what cases I should usually select water molecules and heteroatoms when setting up the protein for binding?
And what is the common way to set the protein up?

Thanks.

Author:  bikadi [ Wed Jul 20, 2011 5:30 pm ]
Post subject:  Re: Selecting Water molecules and hetetoatims

Waters and heteroatoms should be usually omitted. However, there are several example, where structural waters are present in the X-ray, which contributes to binding. If you know about it, you can test docking calculations with waters. Heteroatoms should be choosen for example in cases of metalloproteins or if you want to dock a second ligand into a site.

The most important thing during the protein setup is the correct selection of simulation box. If there is an x-ray ligand at the binding site, then it is easy to select the box, which is done automatically. In other cases you should carefully select the residues in the center of the simulation.

Kind Regards,
Zsolt

Author:  vittuperkele [ Wed Jan 18, 2012 7:39 pm ]
Post subject:  Re: Selecting Water molecules and hetetoatims

bikadi wrote:
The most important thing during the protein setup is the correct selection of simulation box. If there is an x-ray ligand at the binding site, then it is easy to select the box, which is done automatically. In other cases you should carefully select the residues in the center of the simulation.


Hi Zsolt,

Why would the simulation box matter at all if the purpose is doing "blind docking"? say 100*100*100Å for the box size?

Author:  bikadi [ Thu Jan 19, 2012 3:00 pm ]
Post subject:  Re: Selecting Water molecules and hetetoatims

Still in blind docking you should correctly find the appropriate center and size, but you are right that a bit differently - too much vacuum also would decrease the docking efficiency.

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