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Updated: Aug 29, 2025
Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
Published on: June 20, 2025
PyPLIF HIPPOS and Receptor Ensemble Docking Increase the Prediction Accuracy of the Structure-Based Virtual Screening
Enade P Istyastono1, Florentinus Dika Octa Riswanto1, Nunung Yuniarti2
1Faculty of Pharmacy, Sanata Dharma University, Yogyakarta 55282, Indonesia.
Abstract:
In this article, the upgrading process of the structure-based virtual screening (SBVS) protocol targeting acetylcholinesterase (AChE) previously published in 2017 is presented. The upgraded version of PyPLIF called PyPLIF HIPPOS and the receptor ensemble docking (RED) method using AutoDock Vina were employed to calculate the ensemble protein-ligand interaction fingerprints (ensPLIF) in a retrospective SBVS campaign targeting AChE. A machine learning technique called recursive partitioning and regression trees (RPART) was then used to optimize the prediction accuracy of the protocol by using the ensPLIF values as the descriptors. The best protocol resulting from this research outperformed the previously published SBVS protocol targeting AChE.
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