The traditional computational modeling of protein structure, dynamics, and interactions
remains difficult for many protein systems. It is mostly due to the size of protein …

A unified coarse-grained model of three major classes of biological molecules—proteins,
nucleic acids, and polysaccharides—has been developed. It is based on the observations …

In this chapter the scale-consistent approach to the derivation of coarse-grained force fields
developed in our laboratory is presented, in which the effective energy function originates …

Network-based models of proteins are popular tools employed to determine dynamic
features related to the folded structure. They encompass all topological and geometric …

The folding of the N-terminal part of the B-domain of staphylococcal protein A (PDB ID:
1BDD, a 46-residue three-α-helix bundle) and the formin-binding protein 28 WW domain …

Reduction of the representation of macromolecular systems such as, eg biopolymers from
an all-atom to a more crude one, which is termed coarse-graining, is usually regarded as a …

The increasing trend in the recent literature on coarse grained (CG) models testifies their
impact in the study of complex systems. However, the CG model landscape is variegated …

蛋白质-RNA 之间的相互作用是蛋白质在细胞里面行使功能的重要方式之一.
结构生物学家利用实验手段可以得到蛋白质-RNA 复合物的三维结构, 通过原子水平的晶体结构 …

UNRES is a coarse-grained model of polypeptide chains. Until now, each version of UNRES
(UNRESPACK v. 3.2 and earlier ones) has been written in Fortran 77. Due to the fact that …

The knowledge of the three-dimensional structure of proteins is crucial for understanding
many important biological processes. Most of the biologically relevant protein systems are …