eLife

Martinize2 and Vermouth provide a unified framework for molecular topology generation

The authors present an important multi-scale computational platform, which aims to automate the workflow for coarse-grained simulations of biomolecules in the framework of the popular MARTINI model.
eLife

Multi-barrier unfolding of the double-knotted protein, TrmD–Tm1570, revealed by single-molecule force spectroscopy and molecular dynamics

This study investigates the folding and unfolding behavior of the doubly knotted protein TrmD-Tm1570, providing insight into the molecular mechanisms underlying protein knotting. The findings reveal ...
Phys.org

Molecular dynamics simulations use atomistic force field to capture RNA folding with high accuracy

Ribonucleic acid (RNA) is one of life's most versatile molecules, with roles going far beyond being a messenger of genetic code, as it is fundamentally involved in gene regulation, processing, and ...
C&EN

Molecular Dynamics Simulations of RNA Stem-Loop Folding Using an Atomistic Force Field and a Generalized Born Implicit Solvent

Creative Commons (CC): This is a Creative Commons license. Attribution (BY): Credit must be given to the creator.
C&EN

Membrane Protein Simulations

Molecular dynamics (MD) simulations of membrane proteins cover a wide range of applications and specialized techniques. These techniques accurately combine two challenges into one: properly capturing ...