Virtual Screening for Notebook

VDSers – there was some confusion on what to include for Virtual stuff in the Lab Notebook for tomorrow.

For each library you should include a bestranking list and PyMol  images of the Top 10 poses

Then for the first library you screened (HF9 or CB306) and for the final Aggregate run, you need to include the Lipinski’s data for those compounds – it would be best to have this in the same table as the Bestranking list.

You don’t need to include the Lipinski’s data for all of the intermediate libraries.

ALSO, you will need to have the validation dock in there. In order to do that you may need to convert your ligand file from a .mol2 to an .sdf file.

you can do so by typing the following command in the terminal window:

$babel -imol2 myextractedligand.mol2 -osdf myextractedligand.sdf

Obviously, replace ‘myextractedligand’ with the filename of you ligand.

Also – you don’t need the dollar symbol at the front – it is already at the command prompt in the terminal window.

Screening Results

Da’Marcus,

Good question:
You should put your Bestranking Excel sheet for each library.
Then the protocol says to put the image for the Top 10 of each library.
For your Aggregate, it says just to show the images for your Top 5 from the Aggregate that ended up passing all of your Lipinski’s test.
So, that would be good for the Lab Notebook

Thanks,
Dr. B

On Mon, Nov 8, 2010 at 9:16 AM, DaMarcus <dmacxx09@yahoo.com> wrote:
> Dr. B,
>     Do you want us to have images and GOLD Scores for each library screened
> or can we just have the aggregate in the Notebook?
>
> Da’Marcus
>
>

Lab Notebooks graded

Notebooks are graded and in the drawer. See me if you have questions on them.

Thanks,

Dr. B

Reminder: Lab Notebook check for Friday

Lab Notebook Grading Rubric

This rubric will be used to grade the next lab notebook check – which will be this Friday (10/15)

 

https://docs.google.com/fileview?id=0B_Gl3lMyhDsoNzI4NGNiNmEtOWM0Yi00ZjViLTkzYTgtNjE0YzE2ZGIwNjBh&hl=en&authkey=CJOS3xo