NAMD is a parallel molecular dynamics code designed for high‐performance simulation of
large biomolecular systems. NAMD scales to hundreds of processors on high‐end parallel
platforms, as well as tens of processors on low‐cost commodity clusters, and also runs on …

A novel method to flexibly fit atomic structures into electron microscopy (EM) maps using
molecular dynamics simulations is presented. The simulations incorporate the EM data as
an external potential added to the molecular dynamics force field, allowing all internal …

The 26S proteasome is at the executive end of the ubiquitin-proteasome pathway for the
controlled degradation of intracellular proteins. While the structure of its 20S core particle
(CP) has been determined by X-ray crystallography, the structure of the 19S regulatory …

Expression of the Escherichia coli tryptophanase operon depends on ribosome stalling
during translation of the upstream TnaC leader peptide, a process for which interactions
between the TnaC nascent chain and the ribosomal exit tunnel are critical. We determined a …

In translation, elongation factor Tu (EF-Tu) molecules deliver aminoacyl-tRNAs to the mRNA-
programmed ribosome. The GTPase activity of EF-Tu is triggered by ribosome-induced
conformational changes of the factor that play a pivotal role in the selection of the cognate …

The 26S proteasome operates at the executive end of the ubiquitin-proteasome pathway.
Here, we present a cryo-EM structure of the Saccharomyces cerevisiae 26S proteasome at a
resolution of 7.4 Å or 6.7 Å (Fourier-Shell Correlation of 0.5 or 0.3, respectively). We used …

Hybrid computational methods for combining structural data from different sources and
resolutions are becoming an essential part of structural biology, especially as the field
moves toward the study of large macromolecular assemblies. We have developed the …

Cryoelectron tomography provides unprecedented insights into the macromolecular and
supramolecular organization of cells in a close-to-living state. However because of the
limited thickness range (< 0.5–1 μm) that is accessible with today's intermediate voltage …

Protein biosynthesis, the translation of the genetic code into polypeptides, occurs on
ribonucleoprotein particles called ribosomes. Although X-ray structures of bacterial
ribosomes are available, high-resolution structures of eukaryotic 80S ribosomes are lacking …