Gaussian accelerated molecular dynamics (GaMD) is a robust computational method for
simultaneous unconstrained enhanced sampling and free energy calculations of …

Allosteric mechanisms are commonly employed regulatory tools used by proteins to
orchestrate complex biochemical processes and control communications in cells. The …

Calculations of ligand binding free energies and kinetic rates are important for drug design.
However, such tasks have proven challenging in computational chemistry and biophysics …

At the core of the CRISPR–Cas9 genome-editing technology, the endonuclease Cas9
introduces site-specific breaks in DNA. However, precise mechanistic information to …

The powerful CRISPR genome editing system is hindered by its off-target effects, and
existing computational tools achieved limited performance in genome-wide off-target …

CRISPR-Cas9 is a cutting-edge genome editing technology, which uses the endonuclease
Cas9 to introduce mutations at desired sites of the genome. This revolutionary tool is …

In this study, we used an integrative computational approach to examine molecular
mechanisms and determine functional signatures underlying the role of functional residues …

An increasingly pressing need for clinical diagnostics has required the development of novel
nucleic acid-based detection technologies that are sensitive, fast, and inexpensive, and that …

Cas13a is a recent addition to the CRISPR-Cas toolkit that exclusively targets RNA, which
makes it a promising tool for RNA detection. It utilizes a CRISPR RNA (crRNA) to target RNA …

Deciphering the molecular mechanisms of enzymatic allosteric regulation requires the
structural characterization of functional states and also their time evolution toward the …