These results demonstrate a new avenue to determine cryo-EM protein structures with high accuracy and robustness covering various target types and density map resolutions.doi:10.1038/s41592-021-01389-9Xi Zhanggrid.214458.e0000000086837370Department of Computational Medicine and BioinformaticsUniversity of ...
2b), and thus we placed an ideal double-stranded RNA helix (A-form) formed by base-pairing of two separate RNA oligonucleotides into the exit tunnel that fitted well into the cryo-EM density map (Fig. 2a). So far, RNA secondary structure elements in the exit tunnel of RNA polymerases ...
An increasing number of density maps of biological macromolecules have been determined by cryo-electron microscopy (cryo-EM) and stored in the public database, EMDB. To interpret the structural information contained in EM density maps, alignment of maps
2.4 Cryo-EM Map Sharpening Methods 2.5 De Novo Protein Structure Prediction Methods 3. Contributing 4. License 1. Introduction This repository provides a list of the state-of-the-art methods on (i) atomic model building from cryo-EM density maps, (ii) cryo-EM map sharpening, and (iii) de...
我们注意到该数据集包含的蛋白质数量非常少,但事实上DEFMap的输入是cryo-EM density map中的局部结构(尺寸为10Åx10Åx10Å,见图1),因此一个蛋白cryo-EM数据可以拆分成多个训练样本,再加上作者使用了随机旋转进行数据增强,整体数据量能够满足3D卷积神经网络的训练。
DEFMap: Dynamics Extraction From cryo-em Map This package provides an implementation of a dynamics prediction from a cryo-EM density map. Google Colaboratory version of DEFMap is now released. If you want to try it, please visit ColabDEFMap. Dependency Environment Ubuntu: 16.04 or 18.04 (confi...
The initial monomer model of ClC-2 was generated using AlphaFold279, where its flexible loop regions (CBS domain) were deleted before fitting into the cryo-EM density map of ClC-2. As the density of the CBS domain was not good enough for model building, we only manually adjusted the trans...
Segmentation of density maps obtained using cryo-electron microscopy (cryo-EM) is a challenging task, and is typically accomplished by time-intensive inter... GD Pintilie,J Zhang,W Chiu,... 被引量: 7发表: 2009年 Flexible fitting to cryo‐EM density map using ensemble molecular dynamics simula...
Here, as an example, the solution of thestructure of a bacteriophage portal using a partial 30% model built into a 7.8 A˚resolution cryo-EM map is shown. Inspection of the self-rotation functionallowed the correct oligomerization state to be determined, and density-modif i cation procedures...
Lipids with slanted orientations (model in magenta, superimposed on the sharpened density map in light gray; A) are associated with Ca2+-bound TMEM16F in digitonin (green) with lipids (magenta) and one Ca2+ ion (red sphere) in each monomer, overlaid on the electron density map (sharpened...