Towards a Multicomponent Cryo-EM Density Flexible Fitting Tool
نویسندگان
چکیده
منابع مشابه
MVP-Fit: A Convenient Tool for Flexible Fitting of Protein Domain Structures with Cryo-Electron Microscopy Density Map
Summary: MVP-Fit is a visualization tool for interactive fitting atomic protein domain structures with the cryo-Electron Microscopy density map. To achieve the best match, the program can conveniently adjust the loop and tail outliers of individual domains to accommodate the local conformational changes from the rigid-body rotation and translation of protein domains. Availability: The MVP-Fit p...
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 کاملPFfit: 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 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 کاملModel-based local density sharpening of cryo-EM maps
Atomic models based on high-resolution density maps are the ultimate result of the cryo-EM structure determination process. Here, we introduce a general procedure for local sharpening of cryo-EM density maps based on prior knowledge of an atomic reference structure. The procedure optimizes contrast of cryo-EM densities by amplitude scaling against the radially averaged local falloff estimated f...
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ژورنال
عنوان ژورنال: Biophysical Journal
سال: 2017
ISSN: 0006-3495
DOI: 10.1016/j.bpj.2016.11.3094