I am very interested in the VirtualFlow program developed by you and I am learning to use it for drug screening. However, I found there’s no tutorial for VFLP and the documentation for this part is not detailed.Could you please be so kind as to give me some help on how to use it？
Partically,if I downloaded a molecule database(sdf file contain multiple molecules) from other company(eg, chemdiv, chembridge, etc), How do I convert it into a file that can be used by VFLP, and how to prepared it into the different collection in regular directory stucture? (I mean, GA/GACCBF.tar,GA/GACEFF.tar…). It would be very much appreciated if you could also provide a detailed tutorial for the VFLP.
At the moment, we only have the documentation available for VFLP. There is no tutorial yet, but we plan to provide one in the future.
Regarding the input file format for VFLP, the compounds have to be in the SMILES format.
The format of the input ligand library is the same as for VFVS, with the exception that the compounds have to be in the SMILES format instead of the PDBQT format. You can use standard Linux command line tools to prepare the input library, and obabel to convert from SDF to SMILEs for example.
Thank you and I will be looking forward the VFLP tutorial.
By the way, In the file “VFLP-develop/tools/templates/all.ctrl” under VFLP package,
collection_folder=…/…/…/collections/Enamine-REAL-2018q12_isomers.smi.splitted1000_ind_tgz_tar
Could you please share us the file “Enamine-REAL-2018q12_isomers.smi.splitted1000_ind_tgz_tar”? I think that may give us more information how the VFLP input files organised.
the original input library which you mention is many gigabytes, not easy to share.
But the input library structure is exactly the same as the library structure for VFVS (which can be inspected since one can download the libraries from our homepage), except there is one SMILES file instead of one PDBQT File for each ligand.
E.g. the file aspirin.smi could contain the content: