MVP-Fit: A Convenient Tool for Flexible Fitting of Protein Domain Structures with Cryo-Electron Microscopy Density Map
نویسنده
چکیده
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 program and the user manual are freely available at http://zhanglab.ccmb.med.umich.edu/MVP-Fit.
منابع مشابه
FOLD-EM: automated fold recognition in medium- and low-resolution (4-15 Å) electron density maps
MOTIVATION Owing to the size and complexity of large multi-component biological assemblies, the most tractable approach to determining their atomic structure is often to fit high-resolution radiographic or nuclear magnetic resonance structures of isolated components into lower resolution electron density maps of the larger assembly obtained using cryo-electron microscopy (cryo-EM). This hybrid ...
متن کاملFlexible 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...
متن کاملAccurate flexible fitting of high-resolution protein structures into cryo-electron microscopy maps using coarse-grained pseudo-energy minimization.
Cryo-electron microscopy (cryo-EM) has been widely used to explore conformational states of large biomolecular assemblies. The detailed interpretation of cryo-EM data requires the flexible fitting of a known high-resolution protein structure into a low-resolution cryo-EM map. To this end, we have developed what we believe is a new method based on a two-bead-per-residue protein representation, a...
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 کاملFingerprint-based structure retrieval using electron density.
We present a computational approach that can quickly search a large protein structural database to identify structures that fit a given electron density, such as determined by cryo-electron microscopy. We use geometric invariants (fingerprints) constructed using 3D Zernike moments to describe the electron density, and reduce the problem of fitting of the structure to the electron density to sim...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
دوره شماره
صفحات -
تاریخ انتشار 2014