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.
Dear Sir, With due respect, I want a favor from your side. I am working on 3DQSAR pharmacophore modeling study by using 43 inhibitors. I have generated ten hypothesis with good correlation (q2) with the test set. I have used Discovery studio package for this purpose. I want to do decoy set validation test. How should I proceed and which particular protocol of DS2017R2 should I use? I shall be grateful to you if you kindly give me some idea so that I can proceed my work. With best regards Ankur Chaudhuri Research Scholar West Bengal State University Kolkata-700126 India
The search and screen protocols have pretty high throughputs, so I doubt you mean by "select" that you've got so many inactives that you cannot screen them all (?). If this was indeed the case, I would imagine that with only a few simple structural and physico-chemical filters you could reduce the numbers significantly. For example, all your compounds are hydroxamic acids with at least one aromatic ring, fairly low logP and fall in a limited molecular weight range. Discovery Studio offers two "Find Similar Molecules by" protocols that you could use for this.
If, on the other hand, you do not have (enough) inactives for a meaningful challenge, and can't find relevant examples in databases like ChEMBL or PubChem, the next step would be to see whether your target has been covered at one of the existing compilations of benchmarking data sets – you can find a list in  or try EXALEAD / Bing / Google / …). Failing that, you would need to construct one yourself, e.g. following the procedures used for the established decoy collections. This may be a little more straightforward in Pipeline Pilot, but you can also use Discovery Studio, of course. There also exist web services and tools for that task, like DUD-E, RADER or DecoyFinder; I never used any of them, so can't comment on their qualities.
 N.Lagarde, J-F.Zagury, M.Montes: J. Chem. Inf. Model. 55(7) 1297−1307 (2015) link
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.