It would often be useful in computer simulations to use an implicit description of solvation
effects, instead of explicitly representing the individual solvent molecules. Continuum …

CHARMM‐GUI, http://www. charmm-gui. org, is a web‐based graphical user interface that
prepares complex biomolecular systems for molecular simulations. CHARMM‐GUI creates …

Glycolipids (such as glycoglycerolipids, glycosphingolipids, and
glycosylphosphatidylinositol) and lipoglycans (such as lipopolysaccharides (LPS) …

Characterizing glycans and glycoconjugates in the context of three-dimensional structures is
important in understanding their biological roles and developing efficient therapeutic agents …

Motivation Glycans play a central role in many essential biological processes. Glycan
Reader was originally developed to simplify the reading of Protein Data Bank (PDB) files …

Bottom-up multiscale techniques are frequently used to develop coarse-grained (CG)
models for simulations at extended length and time scales but are often limited by a …

Like temperature and pressure, solution pH is an important environmental variable in
biomolecular simulations. Virtually all proteins depend on pH to maintain their structure and …

The interactions between proteins and membranes play critical roles in signal transduction,
cell motility, and transport, and they are involved in many types of diseases. Molecular …

An understanding of the interaction between the antibody and its targeted antigen and
knowing of the epitopes are critical for the development of monoclonal antibody drugs …

Hybrid all-atom/coarse-grained (AA/CG) simulations of proteins offer a computationally
efficient compromise where atomistic details are only applied to biologically relevant regions …