Molecular Docking Server

Stereochemistry at ligand setup
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Author:  vittuperkele [ Mon Jan 16, 2012 7:05 pm ]
Post subject:  Stereochemistry at ligand setup

It seems that after processing a racemic ligand the server randomly chooses the stereochemistry for it (and it cannot be later edited!) Is there any possibility to have a selection after uploading/drawing the ligand(s) to define the appropriate stereo bond to be either r, s or racemic? And would it be possible to automagically do do all the stereoisomers for the docking?

Author:  bikadi [ Mon Jan 16, 2012 7:41 pm ]
Post subject:  Re: Stereochemistry at ligand setup

If you use chiral bonds in drawing ("Single up" and "Single down" in the top left dropdown menu) it should work well. Some enantiomer-making automagic sounds good, I put this task into our todo list :)

Author:  vittuperkele [ Mon Jan 16, 2012 8:49 pm ]
Post subject:  Re: Stereochemistry at ligand setup

Yes, I figured it out after some serious hair pulling. The problem was that when I made a sdf file with chembio-office/Chemsketch, the S's and R's were not the same in the program than in your software :D. It's a feature of those programs, not yours I think. Now I have understood how to draw them "correctly" before doing the sdf.
And when drawing them on the server I always remember to select view --> stereo R/S-labels --> all before clicking ok :)

Anyway -the racemic docking possibility is a must!

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