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Updated: Oct 10, 2025

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
Published on: June 20, 2025
Current Approaches of Building Mechanistic Pharmacodynamic Drug-Target Binding Models
Jingyi Liang1,2,3, Vi Ngoc-Nha Tran1, Colin Hemez4
1Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway.
Abstract:
Mechanistic pharmacodynamic models that incorporate the binding kinetics of drug-target interactions have several advantages in understanding target engagement and the efficacy of a drug dose. However, guidelines on how to build and interpret mechanistic pharmacodynamic drug-target binding models considering both biological and computational factors are still missing in the literature. In this chapter, current approaches of building mechanistic PD models and their advantages are discussed. We also present a methodology on how to select a suitable model considering both biological and computational perspectives, as well as summarize the challenges of current mechanistic PD models.
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