Introducing the Automated Ligand Searcher

The Automated Ligand Searcher (ALISE) is designed as an automated computational drug discovery tool. To approximate the binding free energy of ligands to a receptor, ALISE includes a three-stage workflow, with each stage involving an increasingly sophisticated computational method: molecular docking...

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Bibliographic Details
Published in:Journal of chemical information and modeling 2023-12, Vol.63 (23), p.7518-7528
Main Authors: Jacobsen, Luise, Hungerland, Jonathan, Bačić, Vladimir, Gerhards, Luca, Schuhmann, Fabian, Solov’yov, Ilia A.
Format: Article
Language:English
Subjects:
Computational Biochemistry
Decoys
Drug Discovery
Free energy
Ligands
Molecular docking
Molecular Docking Simulation
Molecular dynamics
Molecular Dynamics Simulation
Protein Binding
Software
Workflow
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Description
Summary:The Automated Ligand Searcher (ALISE) is designed as an automated computational drug discovery tool. To approximate the binding free energy of ligands to a receptor, ALISE includes a three-stage workflow, with each stage involving an increasingly sophisticated computational method: molecular docking, molecular dynamics, and free energy perturbation, respectively. To narrow the number of potential ligands, poorly performing ligands are gradually segregated out. The performance and usability of ALISE are benchmarked for a case study containing known active ligands and decoys for the HIV protease. The example illustrates that ALISE filters the decoys successfully and demonstrates that the automation, comprehensiveness, and user-friendliness of the software make it a valuable tool for improved and faster drug development workflows.
ISSN:1549-9596
1549-960X
1549-960X
DOI:10.1021/acs.jcim.3c01317