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

Biomolecular systems possess unique, structure-encoded dynamic properties that underlie
their biological functions. Recent studies indicate that these dynamic properties are …

Classical simulations of protein flexibility remain computationally expensive, especially for
large proteins. A few years ago, we developed a fast method for predicting protein structure …

The mixed lineage leukaemia (MLL) family of proteins (including MLL1–MLL4, SET1A and
SET1B) specifically methylate histone 3 Lys4, and have pivotal roles in the transcriptional …

A polymer chain of N atoms enjoys 3N-6 internal degrees of freedom, which gives rise to
infinitely many conformations. Even a simple model of N) 100 atoms where bond lengths …

In methanogenic archaea, the carbon dioxide (CO2) fixation and methane-forming steps are
linked through the heterodisulfide reductase (HdrABC)–[NiFe]-hydrogenase (MvhAGD) …

Investigation of macromolecular structure and dynamics is fundamental to understanding
how macromolecules carry out their functions in the cell. Significant advances have been …

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

Protein dynamics is central to all biological processes, including signal transduction, cellular
regulation and biological catalysis. Among them, in-depth exploration of ligand-driven …

Motivation: Dynamic simulations of systems with biologically relevant sizes and time scales
are critical for understanding macromolecular functioning. Coarse-grained representations …