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

Computer simulations are indispensable tools for studying the structure and dynamics of
biological macromolecules. Biochemical processes occur on different scales of length and …

Groningen University, Groningen, Netherlands. MARTINI force field: extension to
carbohydrates We present an extension of the coarse grained (CG) MARTINI force field (1) …

We demonstrate that an external constant electric field is able to modify the secondary
structure of a protein and induce a transition from a β-sheet into a helix-like conformation …

The multiscale coarse-graining (MS-CG) method is used to construct solvent-free CG
models for polyglutamine peptides having various repeat lengths. Because the resulting CG …

We propose the first model of a polypeptide chain based on a hybrid-particle field approach.
The intramolecular potential is built on a two-bead coarse grain mapping for each amino …

We present a generic solvated coarse-grained protein model that can be used to
characterize the driving forces behind protein folding. Each amino acid is coarse-grained …

We study the folding of small proteins inside confining potentials. Proteins are described
using an effective potential model that contains the Ramachandran angles as degrees of …

Amyloid fibril formation is believed to be a nucleation-controlled process. Depending on the
nature of peptide sequence, fibril nucleation can occur in one step, straight from a dilute …

Stable and ordered self-assembled peptide nanostructures are formed as a result of
cooperative effects of various relatively weak intermolecular interactions. We systematically …