Predict the atomic-resolution structure of the conformation described by a density map
Version: 1.0DensityFit combines a low-resolution electronic density map for a protein (usually obtained by electron microscopy) and an atomic-resolution structure (usually obtained by X-ray crystallography) of the same protein in a different conformation in order to predict the atomic-resolution structure of the conformation described by the density map.
Operating System: Mac OS X
This program takes as input a low-resolution electronic density map
(e.g. from electron microscopy) for a protein and a structure of the
same protein in some other conformation.
It then deforms the conformation to fit into the electronic density while preserving the protein structure through the use of low-energy normal modes.
Electron microscopy has become an important tool in structural biology. Many proteins that cannot be made to crystallize in a 3D crystal suitable for X-ray crystallography can nevertheless be studied by electron microscopy, either in the form of 2D crysta
However, the resulting structures have a much lower resolution. With rare exceptions, the electron density maps obtained by electron microscopy are not sufficient to identify the structure at atomic resolution.
In some situations, an atomic-level structure of the same protein in another conformation is available. DensityFit combines this information with the low-resolution structure by deforming the known atomic structure to make it fit into the low-resolution electron density map.
The flexibility of the protein is described by an elastic network model, whose low-energy normal modes define the allowed deformations. This procedure guarantees that the integrity of the protein is preserved during the deformation.