期刊
STRUCTURE
卷 16, 期 5, 页码 673-683出版社
CELL PRESS
DOI: 10.1016/j.str.2008.03.005
关键词
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资金
- NCRR NIH HHS [P41 RR005969-18, P41 RR001219, P41-RR05969, P41-RR01219, P41 RR005969] Funding Source: Medline
- NIGMS NIH HHS [R37 GM029169, R01 GM055440, R01-GM55440, R37-GM29169] Funding Source: Medline
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 added to the molecular dynamics force field, allowing all internal features present in the EM map to be used in the fitting process, while the model remains fully flexible and stereochemically correct. The molecular dynamics flexible fitting (MDFF) method is validated for available crystal structures of protein and RNA in different conformations; measures to assess and monitor the fitting process are introduced. The MDFF method is then used to obtain high-resolution structures of the E coli ribosome in different functional states imaged by cryo-EM.
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