Molecular Informatics [IFM]

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IFM proposes PrepFlow, a new toolkit for chemical library preparation and management. This open-access software is expected to boost the exploitation of big data in Chemistry for structure-based drug discovery.

 

Abstract:

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: https://ifm.chimie.unistra.fr/prep

Reference :

Marion Sisquellas and Marco Cecchini

PrepFlow: A Toolkit for Chemical Library Preparation and Management for Virtual Screening

Molecular Informatics, 2021, DOI:  https://doi.org/10.1002/minf.202100139

 

Contact :

Marco Cecchini, équipe IFM, Institut de Chimie (UMR 7177).