Hi, I am trying to run 3D pharmacophore feature generation protocol but I am not sure how to write values in "Active properties" inside protocol. Every time when I run it shows that "Activity of compounds (list of compounds) is not greater than zero."
What is the format to write and how to solve this problem? Please let me know how to run this protocol.
Hi, I understand, let me explain. You don’t type directly in the Activity Property field in the 3D QSAR protocol parameters. If you open your input ligands .sd file in DS, you can enter the compound activity data into the Data table of the Molecule window. To add a property column: right-click in the Data table and select ‘Add Attribute’ (see screenshot below), give a Name. For example, I call it my_activity. Click OK.
Then you’ll see a new column in the Data table called ‘my_activity’, and you can enter the activity values for each compound in that column. And then when you click in the Activity Propery field in the protocol parameters, you can pick my_activity from the list. That’s all.
In short, the Activity Property parameter is for the user to pick the name of the property containing the molecular activity data. The activity data should be in the input ligands SD file. Hope this is clear.
I am thinking of using molecular dynamics to look at how the entrance to a protein changes overtime and I want to look at it from the angular changes of this opening over the period of the simulations. How do I go about in doing so? Or is that done after I run the simulation?
Hi Kazama, Good Question! You would run the simulation first and then use Analyze Trajectory to perform this type of analysis. Assuming you are using the latest version of Discovery Studio (2017 R2), first load your trajectory by opening the dsv file from the Output folder of your simulation. Next select three atoms that form the angle you wish to monitor. These can be actual atoms or centroids (created by selecting a set of atoms and executing Structure > Monitor > Centroid). Once the three atoms or combination of atoms and centroids are selected, execute the Structure > Monitor > Angle command. Finally, go to the Analyze Trajectory command and enter your molecule. Analysis Type -> Properties, and Properties -> Angle1 (or the name of the Angle property you created). Run the protocol and the output will contain the value of that property for each Conformation in the Trajectory.