By focusing on essential features, while averaging over less important details, coarse-
grained (CG) models provide significant computational and conceptual advantages with …

Protein folding should be complex. Proteins organize themselves into specific three-
dimensional structures, through a myriad of conformational changes. The classical view of …

Recent experimental results suggest that the native fold, or topology, plays a primary role in
determining the structure of the transition state ensemble, at least for small, fast-folding …

Water is essential for life in many ways, and without it biomolecules might no longer truly be
biomolecules. In particular, water is important to the structure, stability, dynamics, and …

Exploring recent developments in the field, Coarse-Graining of Condensed Phase and
Biomolecular Systems examines systematic ways of constructing coarse-grained …

Coarse-grained models are emerging as a practical alternative to all-atom simulations for
the characterization of protein folding mechanisms over long time scales. While a decade …

Determining how a protein folds is a central problem in structural biology. The rate of folding
of many proteins is determined by the transition state, so that a knowledge of its structure is …

Biomolecules often undergo large-amplitude motions when they bind or release other
molecules. Unlike macroscopic machines, these biomolecular machines can partially …

We perform folding simulations on 18 small proteins with using a simple Gō-like protein
model and analyze the folding rate constants, characteristics of the transition state …

Protein recognition and binding, which result in either transient or long-lived complexes,
play a fundamental role in many biological functions, but sometimes also result in pathologic …