An overview of the Amber biomolecular simulation package
R Salomon‐Ferrer, DA Case… - Wiley Interdisciplinary …, 2013 - Wiley Online Library
Molecular dynamics (MD) allows the study of biological and chemical systems at the
atomistic level on timescales from femtoseconds to milliseconds. It complements experiment …
atomistic level on timescales from femtoseconds to milliseconds. It complements experiment …
Self-diffusion coefficient of bulk and confined water: a critical review of classical molecular simulation studies
We present a detailed overview of classical molecular simulation studies examining the self-
diffusion coefficient of water. The self-diffusion coefficient is directly associated with the …
diffusion coefficient of water. The self-diffusion coefficient is directly associated with the …
Higher infectivity of the SARS‐CoV‐2 new variants is associated with K417N/T, E484K, and N501Y mutants: an insight from structural data
The evolution of the SARS‐CoV‐2 new variants reported to be 70% more contagious than
the earlier one is now spreading fast worldwide. There is an instant need to discover how …
the earlier one is now spreading fast worldwide. There is an instant need to discover how …
[HTML][HTML] AlphaFold2 models indicate that protein sequence determines both structure and dynamics
Abstract AlphaFold 2 (AF2) has placed Molecular Biology in a new era where we can
visualize, analyze and interpret the structures and functions of all proteins solely from their …
visualize, analyze and interpret the structures and functions of all proteins solely from their …
Systematic comparison of the structural and dynamic properties of commonly used water models for molecular dynamics simulations
SP Kadaoluwa Pathirannahalage… - Journal of Chemical …, 2021 - ACS Publications
Water is a unique solvent that is ubiquitous in biology and present in a variety of solutions,
mixtures, and materials settings. It therefore forms the basis for all molecular dynamics …
mixtures, and materials settings. It therefore forms the basis for all molecular dynamics …
Hydrolysis of LiPF6-Containing Electrolyte at High Voltage
While lithium hexafluorophosphate (LiPF6) still prevails as the main conducting salt in
commercial lithium-ion batteries, its prominent disadvantage is high sensitivity toward water …
commercial lithium-ion batteries, its prominent disadvantage is high sensitivity toward water …
[HTML][HTML] Ultra-strong bio-glue from genetically engineered polypeptides
The development of biomedical glues is an important, yet challenging task as seemingly
mutually exclusive properties need to be combined in one material, ie strong adhesion and …
mutually exclusive properties need to be combined in one material, ie strong adhesion and …
[HTML][HTML] Adenine oligomer directed synthesis of chiral gold nanoparticles
Precise control of morphology and optical response of 3-dimensional chiral nanoparticles
remain as a significant challenge. This work demonstrates chiral gold nanoparticle synthesis …
remain as a significant challenge. This work demonstrates chiral gold nanoparticle synthesis …
New ways to boost molecular dynamics simulations
E Krieger, G Vriend - Journal of computational chemistry, 2015 - Wiley Online Library
We describe a set of algorithms that allow to simulate dihydrofolate reductase (DHFR, a
common benchmark) with the AMBER all‐atom force field at 160 nanoseconds/day on a …
common benchmark) with the AMBER all‐atom force field at 160 nanoseconds/day on a …
[HTML][HTML] CD4+ effector T cells accelerate Alzheimer's disease in mice
Background Alzheimer's disease (AD) is a progressive neurodegenerative disorder
characterized by pathological deposition of misfolded self-protein amyloid beta (Aβ) which in …
characterized by pathological deposition of misfolded self-protein amyloid beta (Aβ) which in …