Journal
MOLECULAR INFORMATICS
Volume 40, Issue 12, Pages -Publisher
WILEY-V C H VERLAG GMBH
DOI: 10.1002/minf.202100139
Keywords
drug discovery; chemoinformatics; molecular databases; library preparation; workflow; virtual screening
Categories
Funding
- French National Research Agency [ANR-18-CE11-0015]
- Equipex Equip@Meso project (Programme Investissements dAvenir)
- CPER Alsacalcul/Big Data
- Agence Nationale de la Recherche (ANR) [ANR-18-CE11-0015] Funding Source: Agence Nationale de la Recherche (ANR)
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PrepFlow is a toolkit for chemical library preparation and management, which efficiently processes compound lists and outputs 3D molecular structures. The tool excels in execution speed, HPC resource utilization, and archiving strategy, significantly improving the efficiency of drug discovery projects.
In the era of big data in Chemistry, the need for automated tools for virtual screening is compelling. Here, we present PrepFlow a toolkit for chemical library preparation and management. Starting from a list of compounds in SMILES or 2D molecular format, PrepFlow outputs a set of 3D molecular structures ready for use in subsequent drug discovery projects. Our development stands out for speed and robustness of execution, the efficient exploitation of HPC resources, and the implementation of an archiving strategy to save computer time, storage, and human intervention. Using a random selection of 600 compounds from available drug banks, we show that the preparation time per ligand on a desktop computer is 6.6 s. Thanks to these performances and the automatic parallelization on HPC, a chemical library of the size of ChEMBL (2 M) was prepared in around 3 days on a computer cluster. PrepFlow is freely distributed at the following link: .
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