Protein misfolding and aggregation is observed in many amyloidogenic diseases affecting
either the central nervous system or a variety of peripheral tissues. Structural and dynamic …

1.1. The Meaning of “Large Scale” In general, the term “large scale” can have one of the
following five meanings in computational chemistry:(1) large size: power-law and …

RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of
RNA 3D structure prediction. With agreement from crystallographers, the RNA structures are …

RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here
a third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures of riboswitch …

Molecular modeling of proteins including homology modeling, structure determination, and
knowledge-based protein design requires tools to evaluate and refine three-dimensional …

Allosteric transition, defined as conformational changes induced by ligand binding, is one of
the fundamental properties of proteins. Allostery has been observed and characterized in …

As was noted in our recent review, 1 the protein folding field underwent a cyclic
development. Initially, protein folding was viewed as a strictly experimental field belonging to …

Discrete molecular dynamics (DMD) is a rapid sampling method used in protein folding and
aggregation studies. Until now, DMD was used to perform simulations of simplified protein …

Experimental findings suggest that oligomeric forms of the amyloid β protein (Aβ) play a
critical role in Alzheimer's disease. Thus, elucidating their structure and the mechanisms of …

The aggregation of α‐helix‐rich proteins into β‐sheet‐rich amyloid fibrils is associated with
fatal diseases, such as Alzheimer's disease and prion disease. During an aggregation …