An overview of the Amber biomolecular simulation package
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 …
Atomistic simulations of pristine and nanoparticle reinforced hydrogels: A review
Hydrogel is a three‐dimensional cross‐linked hydrophilic network that can imbibe a large
amount of water inside its structure (up to 99% of its dry weight). Due to their unique …
amount of water inside its structure (up to 99% of its dry weight). Due to their unique …
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 …
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 …
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 …
Simulating water with rigid non-polarizable models: a general perspective
Over the last forty years many computer simulations of water have been performed using
rigid non-polarizable models. Since these models describe water interactions in an …
rigid non-polarizable models. Since these models describe water interactions in an …
Flexible simple point-charge water model with improved liquid-state properties
In order to introduce flexibility into the simple point-charge (SPC) water model, the impact of
the intramolecular degrees of freedom on liquid properties was systematically studied in this …
the intramolecular degrees of freedom on liquid properties was systematically studied in this …
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 …