Finding extracted docking poses on the web

VFTools
#1

Hi,

Thank you for using VirtualFlow. Would it be possible to share with me the SD file or SMILES with the structures and IDs to get a better understanding of the issue?

Sincerely,
Yurii

#2

Hey,

here you can download the docking pose output file:

This is the SMILES the output file gives to me:
OC1=NCC@@HC(=O)N1C[C@H]2CCN(C[C@@H]12)C(=O)C(F)F

The compound id:
Compound: PV-000320859287_1_T1

#3

For the second problem, I ran the following command to get a list with the top 100 ligands and their respective docking score, :

head -n 100 ../../ranking/qvina02_rigid_receptor1/firstposes.all.minindex.sorted.clean > compounds

produces compounds

DABCBE_00000 PV-000320859287_1_T1 -8.5 1
BABCBE_00000 Z2763450518_1_T1 -8.3 1
BABCBE_00000 Z32279451_1_T1 -8.3 1
CABCBE_00000 Z2497384867_7_T2 -8.3 1
CABCBE_00001 PV-000548591541_1_T1 -8.3 1
DABCAE_00000 PV-000565564942_1_T1 -8.3 1
etc etc etc

However, after running
vfvs_pp_prepare_dockingposes.sh ../../../output-files/complete/qvina02_rigid_receptor1/results/ meta_collection compounds dockingsposes overwrite

I just get the docking.out.pdbqt like i just sent you, which only contains the poses of the best docked ligand e.g. > DABCBE_00000 PV-000320859287_1_T1 -8.5 1

#4

Hi,

Thank you for sharing the file.
You can look up for the REAL molecules by ID here
https://enaminestore.com/realdb/{ID}

Where {ID} is the original ID. For example, for compound PV-000320859287_1_T1 the original ID is PV-000320859287

As for this particular compound, it has been deprecated in the latest version of the REAL database, because of the reactivity problem of one of the reagents. Therefore, you will not be able to find it in the REAL. You still can request it here libraries@enamine.net and the compound will be quoted not as REAL but as one that requires custom synthesis.
As for the search using SMILES, you can do it here https://enaminestore.com/search#real

#5

Thanks for your answer, yet strange that I cannot see the compound anywhere. So for future projects I must email libraries@enamine.net for all the structures I cnanot find in their database? Because from the given example, all compounds with PV seem to be unavailable.

As for my other problem, do you know whats wrong witth the command? it is only givens me the poses of the best ligand

#6

Hi,

Yes please email send all the structures you can’t find to libraries@enamine.net

As for your other problem, @Christoph will respond to you asap.

#7
Extracting docking poses after the virtual screening