SCEDS: protein fragments for molecular replacement in Phaser.

ABSTRACT: A method is described for generating protein fragments suitable for use as molecular-replacement (MR) template models. The template model for a protein suspected to undergo a conformational change is perturbed along combinations of low-frequency normal modes of the elastic network model. The unperturbed structure is then compared with each perturbed structure in turn and the structurally invariant regions are identified by analysing the difference distance matrix. These fragments are scored with SCEDS, which is a combined measure of the sphericity of the fragments, the continuity of the fragments with respect to the polypeptide chain, the equality in number of atoms in the fragments and the density of C(α) atoms in the triaxial ellipsoid of the fragment extents. The fragment divisions with

SUBMITTER: McCoy AJ 

PROVIDER: S-EPMC3817695 | biostudies-literature | 2013 Nov

REPOSITORIES: biostudies-literature