Advances in the molecular dynamics flexible fitting method for cryo-EM modeling
نویسندگان
چکیده
منابع مشابه
PFfit: Hierarchical Flexible Fitting in 3D EM
We develop a hierarchical solution (PFfit) for fitting an atomic structure to a density map. We use scoring functions that account for steric clashes while maximizing the degree of fit between the protein and the density map, a non-uniform rotationally exhaustive Fourier-based search scheme, and a flexibility model that parametrizes shear and hinge bending motions available to each protein doma...
متن کاملAn Iterative Bézier Method for Fitting Beta-sheet Component of a Cryo-EM Density Map
Cryo-electron microscopy (Cryo-EM) is a powerful technique to produce 3-dimensional density maps for large molecular complexes. Although many atomic structures have been solved from cryo-EM density maps, it is challenging to derive atomic structures when the resolution of density maps is not sufficiently high. Geometrical shape representation of secondary structural components in a medium-resol...
متن کاملDamped-dynamics flexible fitting.
In fitting atomic structures into EM maps, it often happens that the map corresponds to a different conformation of the structure. We have developed a new methodology to handle these situations that preserves the covalent geometry of the structure and allows the modeling of large deformations. The first goal is achieved by working in generalized coordinates (positional and internal coordinates)...
متن کاملRIBFIND: a web server for identifying rigid bodies in protein structures and to aid flexible fitting into cryo EM maps
MOTIVATION To better analyze low-resolution cryo electron microscopy maps of macromolecular assemblies, component atomic structures frequently have to be flexibly fitted into them. Reaching an optimal fit and preventing the fitting process from getting trapped in local minima can be significantly improved by identifying appropriate rigid bodies (RBs) in the fitted component. RESULTS Here we p...
متن کاملProtein-induced membrane curvature investigated through molecular dynamics flexible fitting.
In the photosynthetic purple bacterium Rhodobacter (Rba.) sphaeroides, light is absorbed by membrane-bound light-harvesting (LH) proteins LH1 and LH2. LH1 directly surrounds the reaction center (RC) and, together with PufX, forms a dimeric (RC-LH1-PufX)2 protein complex. In LH2-deficient Rba. sphaeroides mutants, RC-LH1-PufX dimers aggregate into tubular vesicles with a radius of approximately ...
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ژورنال
عنوان ژورنال: Methods
سال: 2016
ISSN: 1046-2023
DOI: 10.1016/j.ymeth.2016.01.009