All soluble proteins populate conformational ensembles that together constitute the native
state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the …

Recently, we saw a dramatic increase in the number of researches that rely on coarse-
grained (CG) simulations for large biomolecules. Here, first, we briefly describe recently …

Molecular dynamics simulations with coarse-grained or simplified Hamiltonians have proven
to be an effective means of capturing the functionally important long-time and large-length …

Proteins perform their biological functions through motion. Although high throughput
prediction of the three-dimensional static structures of proteins has proved feasible using …

For simulating proteins at work in millisecond time scale or longer, we develop a coarse-
grained (CG) molecular dynamics (MD) method and software, CafeMol. At the resolution of …

ABSTRACT Three-dimensional (3D) organization of the human genome plays an essential
role in all DNA-templated processes, including gene transcription, gene regulation, and …

Ligand binding modulates the energy landscape of proteins, thus altering their folding and
allosteric conformational dynamics. To investigate such interplay, calmodulin has been a …

Conspectus Due to hierarchic nature of biomolecular systems, their computational modeling
calls for multiscale approaches, in which coarse-grained (CG) simulations are used to …

Natural protein domains must be sufficiently stable to fold but often need to be locally
unstable to function. Overall, strong energetic conflicts are minimized in native states …

Chromatin organization plays a critical role in cellular function by regulating access to
genetic information. However, understanding chromatin folding is challenging due to its …