Hi,
I am having troubles to download large subset of compounds from the ZINC15 database (1M+ compounds for example). I tried any browser but I consistently get disconnected halfway and there is no way to complete the download.
Anyone with similar issue or suggestions on how to solve this?
Dear Ivan Franzoni
I have attached one link mentioned about the whole procedure. Hope it will solve your query.
https://bioinformaticsreview.com/20200720/how-to-download-small-molecules-for-virtual-screening-from-zinc-database/#:~:text=Go%20to%20the%20download%20page,options%20for%20Linux%20and%20Windows.
Thanks Sourbh Garg - if you download a batch ZINC file yes, the procedure is straightforward and it works pretty well. My problem is with compounds that are classified under different subsections for which no tranches/batches are available.
E.g. https://zinc15.docking.org/majorclasses/epigenetic_regulator/predictions/
Hi, Ivan Franzoni , did you find any way to download structures? If yes, please share your method. I am also in a similar situation.
Best.
Downloading batch file
Go to the download page of the ZINC database.
There you can see multiple options to download such as drug-like, lead-like, clean, and so on.
Select an appropriate category according to your work and download it by clicking on it. A new page will be displayed showing downloading options for Linux and Windows.
Download in MOL2 or SDF format.
If you are downloading for Linux, a csh file will be downloaded whereas, for Windows, a batch file will be downloaded.
Downloading structures
On Ubuntu
Open a terminal (Ctrl+Alt+T).
Change to the directory where you have downloaded the batch file:$ cd Downloads/
$ chmod +x usual.sdf.csh
$ csh usual.sdf.csh
It will download all structures in sdf.gz format.
$ gunzip -v *.sdf.gz. It will provide thousands of structures.
If you want to combine these files into one to ease virtual high-throughput screening, then type the following command: $ cat *.sdf > all_clean.sdf
The batch set can be downloaded easily, but I was looking to download randomly scattered ligands. For instance, I need to download "sorbitol" and "arabinitol". To download these, I need to search for them first, get the link, and simply download them.
Searching and downloading are not supported yet, I think. I tried to work with wiki instructions, but they do not search. If you have any idea of how to search and then download, please let me know.
Hi
You can download custom subset in this way.
https://m.youtube.com/watch?v=0grHHgqZQmE
Due to zinc15 & zinc20 limitations when downloading large datasets, I wrote a script to easily download any zinc15 & zinc20 dataset without any interruptions which can be found in the link below:
https://github.com/shadmehr-gh/zinc_downloader
I hope this helps you.
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