Highlights•Coarse graining allows to model multi-protein aggregates of very large
scale.•Knowledge-based approaches promise to improve protein–protein interface …

Here we report that the rod-like tobacco mosaic virus (TMV), having a negatively charged
surface, can be assembled into three-dimensional micrometer-sized bundle-like …

Coarse-grained (CG) molecular dynamics (MD) simulations allow us to access much larger
length and time scales than atomistic MD simulations, providing an attractive alternative to …

Polysaccharide and proteins are the major constituent building blocks of biological systems
and often occur as highly organized macromolecular architectures (eg the capsid of viruses) …

A high dielectric constant is one of the peculiar properties of liquid water, indicating that the
electrostatic interaction between charged substances is largely reduced in water. We show …

Starch as a food-grade thickener has been commonly used in food products to modulate
textural properties. Improving viscosity-enhancing ability, so as to be able to use less starch …

While coarse-grained (CG) molecular simulations for large biomolecular complexes have
become popular, their electrostatic treatment is often rather simplistic. Here, for C α-based …

The intrinsically disordered protein (IDP) has distinct properties both physically and
biologically: it often becomes folded when binding to the target and is frequently involved in …

Molecular dynamics (MD) simulations using all-atom and explicit solvent models provide
valuable information on the detailed behavior of protein–partner substrate binding at the …

The interior of living cells is densely filled with proteins and their complexes, which perform
multitudes of biological functions. We use coarse-grained simulations to reach the system …