منابع مشابه
Damped-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 کاملDynamics of Flexible Manipulators
This paper presents an application of Continuum (i.e. Lagrangian) and Finite Element Techniques to flexible manipulator arms for derivation of the corresponding Dynamic Equations of Motion. Specifically a one-link flexible arm is considered for detailed analysis, and the results are extended for the case of a two - link flexible manipulator. Numerical examples are given for the case of both one...
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 ...
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 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...
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ژورنال
عنوان ژورنال: Biophysical Journal
سال: 2008
ISSN: 0006-3495
DOI: 10.1529/biophysj.108.132357