Molecular simulation is a powerful computational tool for a broad range of applications
including the examination of materials properties and accelerating drug discovery. At the …

Since its inception nearly a half century ago, CHARMM has been playing a central role in
computational biochemistry and biophysics. Commensurate with the developments in …

Molecular modeling and simulation play important roles in biomedical research as they
provide molecular-level insight into the underlying mechanisms of biological functions that …

The AMOEBA polarizable atomic multipole force field for nucleic acids is presented. Valence
and electrostatic parameters were determined from high-level quantum mechanical data …

Nucleic acid modifications in DNA and RNA ubiquitously exist among all the three kingdoms
of life. This trait significantly broadens the genome diversity and works as an important …

RNAs are central to all gene expression through the control of protein synthesis. Four major
nucleosides, adenosine, guanosine, cytidine and uridine, compose RNAs and provide …

Nonstandard amino acids are both abundant in nature, where they play a key role in various
cellular processes, and can be synthesized in laboratories, for example, for the manufacture …

The ribosome is an RNA-protein complex that is essential for translation in all domains of
life. The structural and catalytic core of the ribosome is its ribosomal RNA (rRNA). While …

The B-DNA double helix can dynamically accommodate GC and AT base pairs in either
Watson–Crick or Hoogsteen configurations. Here, we show that G-C+ (in which+ indicates …

Crucial for mRNA-based vaccines are the composition, structure, and properties of lipid
nanoparticles (LNPs) as their delivery vehicle. Using all-atom molecular dynamics …