[HTML][HTML] Computational biophysics and structural biology of proteins—a Special Issue in honor of Prof. Haruki Nakamura's 70th birthday

D Hall, G Basu, N Ito - Biophysical Reviews, 2022 - Springer
Receiving his initial training jointly in theoretical and applied physics at the University of
Tokyo, Professor Haruki Nakamura has had a long and eventful scientific career, along the …

Editors' Roundup: June 2023

G Basu, Y Sudo, L Berliner, K Shaitan, D Hall - Biophysical Reviews, 2023 - Springer
This commentary article represents the latest edition of the Biophysical Reviews 'Editors'
Roundup'Series—a platform made available to the editorial board members of any journal …

[HTML][HTML] Treatment of flexibility of protein backbone in simulations of protein–ligand interactions using steered molecular dynamics

DT Truong, K Ho, DQH Pham, M Chwastyk… - Scientific Reports, 2024 - nature.com
To ensure that an external force can break the interaction between a protein and a ligand,
the steered molecular dynamics simulation requires a harmonic restrained potential applied …

Calculating Binding Free Energies in Model Host–Guest Systems with Unrestrained Advanced Sampling

AV Marquardt, M Farshad… - Journal of Chemical Theory …, 2024 - ACS Publications
Host–guest interactions are important to the design of pharmaceuticals and, more broadly, to
soft materials as they can enable targeted, strong, and specific interactions between …

Loop Evolutionary Patterns Shape Catalytic Efficiency of TRI101/201 for Trichothecenes: Insights into Protein–Substrate Interactions

Z Yang, N Zhou, X Jiang, L Wang - Journal of Chemical …, 2023 - ACS Publications
Trichothecenes are highly toxic mycotoxins produced by Fusarium fungi, while TRI101/201
family enzymes play a crucial role in detoxification through acetylation. Studies on the …

[PDF][PDF] of the thesis Investigations of Noncanonical Nucleic Acids

Z Zhang - J. Phys. Chem. B, 2021 - is.muni.cz
Noncanonical nucleic acid structures, which play crucial roles in a variety of biological
processes, deserve in-depth investigations. Molecular Dynamics (MD) simulations have …