vktrannguyen / ave-vs-dekois

AVE-vs-DEKOIS

You will find herein the files related to our JCIM viewpoint paper "Beware of Simple Methods for Structure-Based Virtual Screening: The Critical Importance of Broader Comparisons".

Please cite: Tran-Nguyen, V. K.; Ballester, P. J. Beware of Simple Methods for Structure-Based Virtual Screening: The Critical Importance of Broader Comparisons. J. Chem. Inf. Model. 2023, 63, 1401-1405. https://doi.org/10.1021/acs.jcim.3c00218

Two targets namely ACHE (acetylcholinesterase) and HMGR (HMG-CoA reductase) are involved. Each target corresponds to a folder. Inside each folder, you will find the following sub-folders and files:

• DEKOIS sub-folder: training-test partition that employs a DEKOIS2.0 benchmark as test set, experimental data retrieved from PubChem/ChEMBL as training set. AVE split is not involved. Inside this sub-folder are the following files:

  • Mol2 files with the word docked in their names: docked poses of training/test molecules inside their receptor
  • Mol2 files with the word protein in their names: structure of the target used for docking
  • CSV files: information regarding all training/test molecules

• AVE sub-folder: training-test partition that does not employ any pre-existing public benchmark (such as DEKOIS2.0), but only contains experimental data retrieved from PubChem/ChEMBL and DeepCoy-generated decoys property-matched to PubChem/ChEMBL actives. This training-test partition was issued by AVE. Inside this sub-folder are the following files:

  • Mol2 and CSV files: similarly to those in the DEKOIS sub-folder
  • SMI files: the input and output files of AVE
  • TXT file: information regarding the AVE split process

We also provide herein the script for carrying out AVE split (Remove_AVE_Python3.py). This script has been modified from the original version written by AVE authors (https://doi.org/10.1021/acs.jcim.7b00403) to be able to run in Python 3.

For more information, please contact Dr. Viet-Khoa Tran-Nguyen ([email protected]) or Dr. Pedro J. Ballester ([email protected]).