The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has recently emerged
in China and caused a disease called coronavirus disease 2019 (COVID-19). The virus …

Proteins are dynamic entities that undergo a plethora of conformational changes that may
take place on a wide range of time scales. These changes can be as small as the rotation of …

ProDy, an integrated application programming interface developed for modelling and
analysing protein dynamics, has significantly evolved in recent years in response to the …

The functions of many proteins are regulated through allostery, whereby effector binding at a
distal site changes the functional activity (eg, substrate binding affinity or catalytic efficiency) …

By focusing on essential features, while averaging over less important details, coarse-
grained (CG) models provide significant computational and conceptual advantages with …

Liquid–liquid phase separation (LLPS) is an important mechanism that helps explain the
membraneless compartmentalization of the nucleus. Because chromatin compaction and …

Phaser is a program for phasing macromolecular crystal structures by both molecular
replacement and experimental phasing methods. The novel phasing algorithms …

Abstract CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and
widely used molecular simulation program. It has been developed over the last three …

Connecting the molecular world to biology requires understanding how molecular-scale
dynamics propagate upward in scale to define the function of biological structures. To …

Although algebraic graph theory-based models have been widely applied in physical
modeling and molecular studies, they are typically incompetent in the analysis and …