{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Jacobsen L"],"funding":["Nieders?chsisches Ministerium f?r Wissenschaft und Kultur","Deutsche Forschungsgemeinschaft","Danmarks Frie Forskningsfond","Volkswagen Foundation"],"pagination":["7518-7528"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC10716895"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["63(23)"],"pubmed_abstract":["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"],"journal":["Journal of chemical information and modeling"],"pubmed_title":["Introducing the Automated Ligand Searcher."],"pmcid":["PMC10716895"],"funding_grant_id":["SFB 1372","514664767","GRK1885","TRR 386/1-2023"],"pubmed_authors":["Bacic V","Schuhmann F","Jacobsen L","Gerhards L","Solov'yov IA","Hungerland J"],"additional_accession":[]},"is_claimable":false,"name":"Introducing the Automated Ligand Searcher.","description":"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","dates":{"release":"2023-01-01T00:00:00Z","publication":"2023 Dec","modification":"2026-05-28T22:24:26.095Z","creation":"2025-04-04T21:20:07.228Z"},"accession":"S-EPMC10716895","cross_references":{"pubmed":["37983165"],"doi":["10.1021/acs.jcim.3c01317"]}}