Hui Sun Lee

TL;DR: The output from Ligand Reader & Modeler can be used in other CHARMM‐GUI modules to build a protein‐ligand simulation system for all supported simulation programs, such as CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM.

TL;DR: A computational tool, Glycan Modeler for in silico N-/O-glycosylation of the target protein and generation of carbohydrate-only systems and the structural properties of modeled glycan structures investigated by running 2-μs molecular dynamics simulations of HIV envelope protein.

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: This study reveals that N-glycosylation does not induce significant changes in protein structure, but decreases protein dynamics, likely leading to an increase in protein Stability, suggesting a need for certain proteins to be properly glycosylated to gain their intrinsic dynamic properties.

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.