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SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields.
- J. Frank, M. Radermacher, +4 authors A. Leith
- Computer Science, Medicine
- Journal of structural biology
The SPIDER system has evolved into a comprehensive tool set for image processing, making use of modern graphics interfacing in the VMS and UNIX environment. Expand
Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics.
- Leonardo G. Trabuco, E. Villa, Kakoli Mitra, J. Frank, K. Schulten
- Chemistry, Medicine
- 7 May 2008
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… Expand
Three-Dimensional Electron Microscopy of Macromolecular Assemblies: Visualization of Biological Molecules in Their Native State
- J. Frank
- 26 January 1996
Cryoelectron microscopy of biological molecules is among the hottest growth areas in biophysics and structural biology at present, and Frank is arguably the most distinguished practitioner of this… Expand
Structure of the 80S Ribosome from Saccharomyces cerevisiae—tRNA-Ribosome and Subunit-Subunit Interactions
A cryo-EM reconstruction of the translating yeast 80S ribosome was analyzed. Computationally separated rRNA and protein densities were used for docking of appropriately modified rRNA models and… Expand
SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs
This protocol describes the reconstruction of biological molecules from the electron micrographs of single particles. Computation here is performed using the image-processing software SPIDER and can… Expand
Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation
An 11.7‐Å‐resolution cryo‐EM map of the yeast 80S·eEF2 complex in the presence of the antibiotic sordarin was interpreted in molecular terms, revealing large conformational changes within eEF2 and… Expand
The Cryo-EM Structure of a Translation Initiation Complex from Escherichia coli
The 70S ribosome and its complement of factors required for initiation of translation in E. coli were purified separately and reassembled in vitro with GDPNP, producing a stable initiation complex… Expand
Architecture of the Protein-Conducting Channel Associated with the Translating 80S Ribosome
In vitro assembled yeast ribosome-nascent chain complexes (RNCs) containing a signal sequence in the nascent chain were immunopurified and reconstituted with the purified protein-conducting channel… Expand
Structure of the signal recognition particle interacting with the elongation-arrested ribosome
Cotranslational translocation of proteins across or into membranes is a vital process in all kingdoms of life. It requires that the translating ribosome be targeted to the membrane by the signal… Expand
Molecular architecture of the human pre-mRNA 3' processing complex.
- Y. Shi, D. Di Giammartino, +5 authors James L. Manley
- Biology, Medicine
- Molecular cell
- 13 February 2009
Pre-mRNA 3' end formation is an essential step in eukaryotic gene expression. Over half of human genes produce alternatively polyadenylated mRNAs, suggesting that regulated polyadenylation is an… Expand