Introducing the Automated Ligand Searcher

Luise Jacobsen, Jonathan Hungerland, Vladimir Bačić, Luca Gerhards, Fabian Schuhmann*, Ilia A. Solov’yov*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

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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.

Original languageEnglish
JournalJournal of Chemical Information and Modeling
Issue number63
Pages (from-to)7518–7528
Number of pages11
Publication statusPublished - 2023


  • Drug Discovery
  • Ligands
  • Molecular Docking Simulation
  • Molecular Dynamics Simulation
  • Protein Binding
  • Software


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