但是由于结合抗体的多克隆性质和cryoEMPEM map的分辨率约为3到4埃,仅凭结构信息难以直接确定抗体序列。==作者假设如果能够获取适当的序列数据库==,在这个序列数据库中包含与采集血清(即pAb)的时间点相匹配的B细胞受体库(BCR),那么就可以利用cryoEMPEM中的含有的pAb的结构信息,从BCR库中选择出重链和轻链的候选者。
for analyzing EM maps, including rigid-body structure fitting of atomic models5, comparison of maps to identify differences in maps during a structure modeling process6or to understand similarities and differences of different functional states7,8,9, and EM map database search10,11. Two types of...
Figure 1: CryoEM map of ZIKV/ZIKV-117. From:A human antibody against Zika virus crosslinks the E protein to prevent infection The ZIKV-Fab surface is shown in radial colouring, from yellow (∼210 Å) to red (∼290 Å). The bound Fab (red ‘knobs’) extends from the surfac...
cryoEM map – C15 Barrel https://www.ebi.ac.uk/pdbe/emdb/ EMD-21154 PDB model – C15 PilQ https://www.rcsb.org 6VE4 Experimental models: cell lines P. aeruginosa mPAO1 (Jacobs et al., 2003) N/A PAO1 ΔtsaP [Deletion of tsaP] This Study N/A P. aeruginosa PAO1 ΔpilN [Tra...
For atomic-level dynamics visualization, DEFMap needs a PDB file corresponding to the cryo-EM map used for inference. Scale voxel length and map resolution cd preprocessing python rescale.py -l ../data/sample_pdb_map.list -s 1.5 -r 5 Create dataset python prep_dataset.py -m ../data...
Deng Luo, Zainab Alsuwaykit, Dawar Khan, Ondřej Strnad, Tobias Isenberg, and Ivan Viola. DiffFit: Visually-Guided Differentiable Fitting of Molecule Structures to a Cryo-EM Map. IEEE Transactions on Visualization and Computer Graphics, 31, 2025. To appear. doi:10.1109/TVCG.2024.3456404 ...
Multiple models describe conformational variability of an EM map • Multi-model pipeline uses freely available software, assessed over 300 EMDB entries • Generated a standardized suite of EM maps at a range of resolutions < 5Å Summary There does not currently exist a standardized indicator of...
This map challenge was one of two community-wide challenges sponsored by EMDataBank in 2015/2016 to critically evaluate 3DEM methods that are coming into use, with the ultimate goal of developing validation criteria associated with every 3DEM map and map-derived model. 展开 ...
ARTICLE https://doi.org/10.1038/s41467-020-20295-w OPEN FSC-Q: a CryoEM map-to-atomic model quality validation based on the local Fourier shell correlation Erney Ramírez-Aportela 1✉, David Maluenda1, Yunior C. Fonseca1, Pablo Conesa1, Roberto Marabini2, J. Bernard Heymann 3, Jose ...