DensityFit

DensityFit is a software that allows you to predict the atomic-resolution structure of a protein by combining a low-resolution electronic density map and an atomic-resolution structure of the same protein but in a different conformation. This program takes in a low-resolution electronic density map obtained from electron microscopy and a structure of the same protein in a different conformation. It then uses low-energy normal modes to deform the conformation to fit into the electronic density map while preserving the protein structure.

Electron microscopy has become a vital tool in structural biology, especially for proteins that cannot be crystallized in 3D crystal suitable for X-ray crystallography. The structures obtained from electron microscopy have lower resolution, and the electron density maps are insufficient to identify the structure at atomic resolution. However, in some cases, an atomic-level structure of the same protein in another conformation is available, and DensityFit can use this information to combine with the low-resolution structure, deforming the known atomic structure to fit into the low-resolution electron density map.

To describe the flexibility of the protein, DensityFit uses an elastic network model, and its low-energy normal modes define the allowed deformations. This procedure ensures that the protein's integrity is preserved during the deformation. Overall, DensityFit is a powerful tool for predicting the atomic-resolution structure of a protein, especially when using a low-resolution electron density map obtained from electron microscopy.