Huan Rui

TL;DR: The new features and major improvements in Membrane Builder that allow users to robustly build realistic biological membrane systems are described, including addition of new lipid types, including phosphoinositides, cardiolipin (CL), sphingolipids, bacterial lipids, and ergosterol.

TL;DR: The C36 CHARMM lipid force field has been extended to include sphingolipids, via a combination of high-level quantum mechanical calculations on small molecule fragments, and validation by extensive molecular dynamics simulations on N-palmitoyl and N-stearoyl sphingomyelin.

TL;DR: Recently, new modules have been integrated into CHARMM‐GUI, such as Glycolipid Modeler for generation of various glycolIPid structures, and LPS Modelerfor generation of lipopolysaccharide structures from various Gram‐negative bacteria.

TL;DR: Functionalities that have recently been integrated into CHARMM-GUI PDB Manipulator are described, such as ligand force field generation, incorporation of methanethiosulfonate spin labels and chemical modifiers, and substitution of amino acids with unnatural amino acids to be useful in advanced biomolecular modeling and simulation of proteins.

TL;DR: To explore the energetics and mechanism of passive cholesterol flip-flop and its dependence on chain saturation, two-dimensional umbrella sampling simulations in DPPC, POPC, and DAPC are performed and the resulting paths indicate that cholesterol prefers to tilt first and then move to the bilayer center where the free energy barrier exists.