Evaluation Test Maps: 36 EM maps from multiple angles Resolution: 17 maps (3-4A), 14 maps (4-5.5A) Protein Secondary Structure: 9 maps (helix-rich), 9 maps (sheet-rich), 18 maps (equally helix&strand-rich) 3 Improvement of local map regions by SuperEM Local and global map resolution...
The interpretation of high-resolution cryo electron microscopy (cryo-EM) maps relies on the creation of precise atomic models that help analyzing the detailed interactions within a macromolecular complex. In the accompanying paper to this protocol, we describe the high-resolution structure of the ...
Simply speaking, DeepEMhancer performs a non-linear post-processing of cryo-EM maps that produces two main effects: Local sharpening-like post-processing. Automatic masking/denoising of cryo-EM maps. Table of Contents INSTALLATION USAGE GUIDE ...
DiMaio, RosettaES: a sampling strategy enabling automated interpretation of difficult cryo-EM maps. Nat. Methods. in press (2017).Frenz, B., Walls, A. C., Egelman, E. H., Veesler, D., and DiMaio, F. (2017) RosettaES: a sampling strategy enabling automated interpretation of dif- ...
CryoSPARC is a globally trusted complete solution for cryo-EM data processing Ultra-fast end-to-end processing of raw cryo-EM data and reconstruction of electron density maps, ready for ingestion into model building software Optimized algorithms and GPU acceleration at all stages, from pre-processing...
{3}, number = {2}, pages = {153--160}, author = {Shigeyuki Matsumoto and Shoichi Ishida and Mitsugu Araki and Takayuki Kato and Kei Terayama and Yasushi Okuno}, title = {Extraction of protein dynamics information from cryo-{EM} maps using deep learning}, journal = {Nature Machine ...
Automatic ultrastructure segmentation of reconstructed CryoEM maps of icosahedral viruses We present an automatic algorithm to segment all the local and global asymmetric units of a three-dimensional density map of icosahedral viruses. This appr... Z Yu,C Bajaj - 《IEEE Transactions on Image Processi...
Interpretation of cryo-electron microscopy (cryo-EM) maps requires building and fitting 3-D atomic models of biological molecules. AlphaFold-predicted models generate initial 3-D coordinates; however, model inaccuracy and conformational heterogeneity often necessitate labor-intensive manual model building and...
This characterization would benefit from making available all density maps where local refinement has been performed, as done for the map of the apo state (EMDB 24465). The presence of CaM in the sample may be explained by the relatively high abundance of endogenous CaM in HEK cells, which ...
An increasing number of density maps of macromolecular structures, including proteins and DNA/RNA complexes, have been determined by cryo-electron microscopy (cryo-EM). Although lately maps at a near-atomic resolution are routinely reported, there are still substantial fractions of maps determined at...