From Quantum Mechanics, Classical Mechanics, and Bioinformatics to Artificial Intelligence Studies in Neurodegenerative Diseases
Document Type
Book Chapter
Publication Date
2022
Keywords
DFT, CPMD Simulations, T-REMD Simulations, Disorder Predictors, Deep Learning
Digital Object Identifier (DOI)
https://doi.org/10.1007/978-1-0716-1546-1_8
Abstract
The amyloid β-protein is an intrinsically disordered protein that has the potential to assemble into myriad structures, including oligomers and fibrils. These structures are neurotoxic and are thought to initiate a cascade of events leading to Alzheimer’s disease. Understanding this pathogenetic process and elucidating targets for drug therapy depends on elucidation of the structural dynamics of Aβ assembly. In this chapter, we describe work packages required to determine the three-dimensional structures of Aβ and of smaller bioactive fragments thereof, which may be important in AD pathogenesis. These packages include density functional theory, Car–Parrinello molecular dynamics simulations, temperature-dependent replica exchange molecular dynamics simulations, disorder predictors based on bioinformatics, and neural network deep learning.
Was this content written or created while at USF?
Yes
Citation / Publisher Attribution
From Quantum Mechanics, Classical Mechanics, and Bioinformatics to Artificial Intelligence Studies in Neurodegenerative Diseases, M. S. Li, A. Kloczkowski, M. Cieplak & M. Kouza (Eds.), Computer Simulations of Aggregation of Proteins and Peptides, Humana Press, p. 139-173
Scholar Commons Citation
Coskuner-Weber, Orkid; Habiboglu, M. Gokhan; Teplow, David; and Uversky, Vladimir N., "From Quantum Mechanics, Classical Mechanics, and Bioinformatics to Artificial Intelligence Studies in Neurodegenerative Diseases" (2022). Molecular Medicine Faculty Publications. 978.
https://digitalcommons.usf.edu/mme_facpub/978
