The poly-l-proline type II (PPII) helix in recent years has emerged clearly as a structural class
not only of fibrillar proteins (in collagen, PPII is a dominant conformation) but also of the …

Many gene sequences in eukaryotic genomes encode entire proteins or large segments of
proteins that lack a well-structured three-dimensional fold. Disordered regions can be highly …

Development of the AMOEBA (atomic multipole optimized energetics for biomolecular
simulation) force field for proteins is presented. The current version (AMOEBA-2013) utilizes …

The ff94 force field that is commonly associated with the Amber simulation package is one of
the most widely used parameter sets for biomolecular simulation. After a decade of …

Molecular mechanics models have been applied extensively to study the dynamics of
proteins and nucleic acids. Here we report the development of a third-generation point …

Obtaining the correct balance of secondary structure propensities is a central priority in
protein force-field development. Given that current force fields differ significantly in their α …

Recent reports give strong support to the idea that amyloid fibril formation and the
subsequent development of protein deposition diseases originate from conformational …

Several proteomic studies in the last decade revealed that many proteins are either
completely disordered or possess long structurally flexible regions. Many such regions were …

The application of Raman spectroscopy to characterize natively unfolded proteins has been
underdeveloped, even though it has significant technical advantages. We propose that a …

The ensemble folding of two 21-residue α-helical peptides has been studied using all-atom
simulations under several variants of the AMBER potential in explicit solvent using a global …