search

Shen-Lab / DeepAffinity

Protein-compound affinity prediction through unified RNN-CNN
GNU General Public License v3.0
137 stars 30 forks source link

No BindingDB_All.tsv exists. #8

Closed CallMeDek closed 2 years ago

CallMeDek commented 2 years ago

Hi,

Thank you for your work. I am following your work with "DeepAffinity/data/script/split_data_script/README.md" But there is a problem. According to README.md, there must be BindingDB_All.tsv in google drive(https://drive.google.com/open?id=1_uZVTBVPeeF64joitPU8uDZnfIGS1me0). But there's no tsv file exist instead only BindingDB_ALL_2D.sdf is available. So, I can't proceed anymore.

Thank you Dek

Shen-Lab commented 2 years ago

Hi @CallMeDek, Thank you for your interest in DeepAffinity. You are right in finding the link wrong for the file needed, BindingDB_All.tsv, for firstStep.py. Instead the file can be downloaded from bindingdb.org. Simply proceeds to Download and find the corresponding file in the latest version. For instance, the latest as of today is the 2022-09-01 version called "BindingDB_All_2022m8.tsv.zip". Unfortunately we cannot locate the version we used "BindingDB_All_2018m8.tsv.zip" at this moment. If that version is critical, I am reaching @AstroSign and I have also contacted BindingDB, but there is no guarantee. Our apologies for any inconvenience this may cause to you.

Thanks again, DeepAffinity Team

CallMeDek commented 2 years ago

Hi, DeepAffinity Team

Thank you for your reply. I was able to find the latest version of tsv file in bindingdb.org. I am trying to get a result with the file.

Thanks, Dek