Targeted conformational search with map-restrained self-guided Langevin dynamics: Application to flexible fitting into electron microscopic density maps
نویسندگان
چکیده
منابع مشابه
Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics.
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 corr...
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Combining X-ray crystallographically determined atomic structures of component domains or subunits with cryo-electron microscopic three-dimensional images at around 22 A resolution can produce structural information that is accurate to about 2.2 A resolution. In an initial step, it is necessary to determine accurately the absolute scale and absolute hand of the cryo-electron microscopy map, the...
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The charge density (CD) distribution of an atom is the difference per unit volume between the positive charge of its nucleus and the distribution of the negative charges carried by the electrons that are associated with it. The CDs of the atoms in macromolecules are responsible for their electrostatic potential (ESP) distributions, which can now be visualized using cryo-electron microscopy at h...
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A systematic search approach to the automatic refinement of protein structures could reduce the need for manual intervention. In this approach, possible conformations for a segment of the polypeptide chain are generated systematically and the trial segments are scored for their agreement with the observed diffraction data. The sampling of conformational space is sufficiently exhaustive that rea...
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Molecular replacement is a powerful tool for the location of large models using structure-factor magnitudes alone. When phase information is available, it becomes possible to locate smaller fragments of the structure ranging in size from a few atoms to a single domain. The calculation is demanding, requiring a six-dimensional rotation and translation search. A number of approaches have been dev...
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ژورنال
عنوان ژورنال: Journal of Structural Biology
سال: 2013
ISSN: 1047-8477
DOI: 10.1016/j.jsb.2013.07.006