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PrepFlow: A Toolkit for Chemical Library Preparation and Management for Virtual Screening
- Source :
- Molecular Informatics. 40:2100139
- Publication Year :
- 2021
- Publisher :
- Wiley, 2021.
-
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/prepflow.
- Subjects :
- Computer science
Big data
Ligands
01 natural sciences
Chemical library
Small Molecule Libraries
03 medical and health sciences
chemistry.chemical_compound
Structural Biology
Computer cluster
Drug Discovery
Humans
030304 developmental biology
0303 health sciences
Virtual screening
business.industry
Organic Chemistry
chEMBL
0104 chemical sciences
Computer Science Applications
010404 medicinal & biomolecular chemistry
Automatic parallelization
Workflow
chemistry
Cheminformatics
Molecular Medicine
Software engineering
business
Subjects
Details
- ISSN :
- 18681751 and 18681743
- Volume :
- 40
- Database :
- OpenAIRE
- Journal :
- Molecular Informatics
- Accession number :
- edsair.doi.dedup.....c641784c1dd27d0b9e2ed70c9f6472be