.png){kind=icon}
返回
Automated cryo-EM structure refinement using correlation-driven molecular dynamics
.png){kind=icon}
OA
AI
DOI：10.7554/eLife.43542.png)
.png){kind=icon}
原文求助.png){kind=icon}
分享.png){kind=icon}
收藏
摘要
En 中文
We present a correlation-driven molecular dynamics (CDMD) method for automated refinement of atomistic models into cryo-electron microscopy (cryo-EM) maps at resolutions ranging from near-atomic to subnanometer. It utilizes a chemically accurate force field and thermodynamic sampling to improve the real-space correlation between the modeled structure and the cryo-EM map. Our framework employs a gradual increase in resolution and map-model agreement as well as simulated annealing, and allows fully automated refinement without manual intervention or any additional rotamer-and backbone-specific restraints. Using multiple challenging systems covering a wide range of map resolutions, system sizes, starting model geometries and distances from the target state, we assess the quality of generated models in terms of both model accuracy and potential of overfitting. To provide an objective comparison, we apply several wellestablished methods across all examples and demonstrate that CDMD performs best in most cases.
Keyword:
MUSCLE FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE
DEPENDENT ROTAMER LIBRARY
CRYOELECTRON MICROSCOPY
FORCE-FIELD
RESOLUTION STRUCTURE
PROTEIN-STRUCTURE
MODEL
PARTICLE
PHENIX
DOMAIN
期刊
IF:
0
论文数:
1.8W
被引数:
16
机构
引用论文
Resilient Peer-to-Peer live-streaming using motifs.png)
2010 IEEE International Symposium on "A World of Wireless, Mobile and Multimedia Networks" (WoWMoM)
2010 IEEE International Symposium on "A World of Wireless, Mobile and Multimedia Networks" (WoWMoM)IF0
PREAI
分享收藏Flexible fitting to cryo-EM density map using ensemble molecular dynamics simulations使用集成分子动力学模拟灵活拟合cryo-em密度图
PREAI
分享收藏
Automated structure refinement of macromolecular assemblies from cryo-EM maps using RosettaELIFEOAAI
ELIFEIF0
OAAI分享收藏
查看更多内容