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Replica exchange of expanded ensembles: A generalized ensemble approach with enhanced flexibility and parallelizability
In this paper, we developed a new alchemcal free energy method that addresses the limitations of expanded ensemble and Hamiltonian replica exchange by combining the two methods.
Wei-Tse Hsu, Miahael R. Shirts
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Alchemical metadynamics: Adding alchemical variables to metadynamics to enhance sampling in free energy calculations
In this paper, we developed a new advanced sampling method that could address the challenges that fail traditional alchemical free energy methods.
Wei-Tse Hsu, Valerio Piomponi, Pascal T. Merz, Giovanni Bussi, Miahael R. Shirts
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Identifying signatures of proteolytic stability and monomeric propensity in O-glycosylated insulin using molecular simulation
Based on data from molecular dynamics, we devloped a screening method for glycosylated insulin analogs with higher proteolytic stability and lower dimerization propensity.
Wei-Tse Hsu, Dominique A. Ramirez, Tarek Sammakia, Zhongping Tan, Michael R. Shirts
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physical_validation: A Python package to assess the physical validity of molecular simulation results
In this shorts paper, we updated physical_validation, which is a Python package testing results obtained from molecular simulations for theiry physical validity.
Pascal T. Merz, Wei-Tse Hsu, Matt W. Thompson, Simon Boothroyd, Chris C. Walker, Michael R. Shirts
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Exploring the influence of brilliant blue G on amyloid fibril formation of lysozyme
Evidence suggests that amyloid fibril mitigation/inhibition is considered a promising approach toward treating amyloid diseases. In …
Su-Chun How, Ai Hsin, Guan-Yu Chen, Wei-Tse Hsu, Szu-Ming Yang, Wei-Lung Chou, Shiu-Huey Chou, Steven S.-S. Wang
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Lysozyme amyloid fibrillization in presence of tacrine/acridone-coumarin heterodimers
Amyloid aggregates of proteins are one of the most abundant and important naturally occurring self-associated assemblies. Formation of …
Katarina Ulicna, Zuzana Bednarikova, Wei-Tse Hsu, Martina Holztragerova, Josephine W Wu, Slavka Hamulakova, Steven S.-S. Wang, Zuzana Gazova
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Brilliant blue R dye is capable of suppressing amyloid fibril formation of lysozyme
Amyloid fibril formation is associated with an array of degenerative diseases. While no real cure is currently available, evidence …
Su-Chun How, Wei-Tse Hsu, Chia-Ping Tseng, Chun-Hsien Lo, Wei-Lung Chou, Steven S.-S. Wang
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Investigating the effects of erythrosine B on amyloid fibril formation derived from lysozyme
Formation of amyloid fibrils has been associated with at least 30 different protein aggregation diseases. The 129-residue polypeptide …
Chun-Tien Kuo, Yi-Lin Chen, Wei-Tse Hsu, Su-Chun How, Yu-Hong Cheng, Shu-Shun Hsueh, Hwai-Shen Liu, Ta-Hsien Lin, Josephine W Wu, Steven S.-S. Wang
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