MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes

Abstract

MolProbity is a general-purpose web service offering quality validation for three-dimensional (3D) structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules and can calculate and display the H-bond and van der Waals contacts in the interfaces between components. An integral step in the process is the addition and full optimization of all hydrogen atoms, both polar and nonpolar. The results are reported in multiple forms: as overall numeric scores, as lists, as downloadable PDB and graphics files, and most notably as informative, manipulable 3D kinemage graphics shown on-line in the KiNG viewer. This service is available free to all users at http://kinemage.biochem.duke.edu.

Figure 1

All-atom contacts used to assess structure quality for hammerhead ribozymes, as calculated in MolProbity and displayed online in the KiNG Java viewer. (a) Well-fit base–base and base–backbone interactions (see Methods for color code) in the tetraloop region of the 359D/urx067 structure (14). (b) Overview of the 359D/urx067 backbone, showing just the serious steric clashes (red spikes); its clash score is 55. (c) Overview of the similar 379D/urx071 backbone (19), showing just the serious clashes; its clash score is 139, and the clashes are not in the same positions.

Figure 2

The main page of the MolProbity server during a session analyzing the 1HQ1/pr0037 protein–RNA complex (20), with a rotatable thumbnail image at the top, contact and geometry analysis tools in the center and control of file uploads and downloads at the bottom.

Figure 3

All-atom contacts for the interface between ribosomal protein L23 (on left, in peach) and a four-way junction region of the 23S RNA (on right, with white backbone and cyan bases), from the 1JJ2/rr0033 structure of the 50S ribosomal subunit from Haloarcula xmarismortui (15). Only two bases are involved, almost all contact being between protein side chains and the RNA backbone. (See Methods for color coding of the dot surfaces.)