MolProbity: all-atom contacts and structure validation for proteins and nucleic acids

Abstract

MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules as well as updated dihedral-angle diagnostics, and it 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. New analysis functions have been added for RNA, for interfaces, and for NMR ensembles. Additionally, both the web site and major component programs have been rewritten to improve speed, convenience, clarity and integration with other resources. MolProbity results are reported in multiple forms: as overall numeric scores, as lists or charts of local problems, as downloadable PDB and graphics files, and most notably as informative, manipulable 3D kinemage graphics shown online in the KiNG viewer. This service is available free to all users at http://molprobity.biochem.duke.edu.

Figure 1.

Multi-criterion chart for 2J21, a crystal structure of the p53 DNA-binding core domain (37). The chart shows both overall statistics (top) and the first 20 residues of local data. Although a few steric clashes and one rotamer outlier are visible here (pink boxes) and might be worth trying to fix, this is an excellent structure overall; its resolution is 1.6Å, and compared to other structures at similar resolution, it ranks in the 92nd percentile for overall quality (MolProbity score).

Figure 2.

Multi-criterion kinemage of a 5-model NMR ensemble in side-by-side stereo, displayed in the KiNG applet. A small peptide (yellow) is bound to a short RNA hairpin (black), in file 1BIV (38). MolProbity has highlighted steric clashes (pink spikes), suspect RNA sugar puckers (magenta T's), outlier conformations of protein backbone (green) and sidechains (gold) and deviant bond angles around protein Cα's (magenta balls). On the right side, KiNG has controls for turning on or off the individual models, parts of the molecules (protein versus nucleic acid, Calphas versus full backbone, etc.) and validation criteria.

Figure 3.

Run-time distributions: improvement for the new version of Reduce. Optimizing hydrogens by exhaustive enumeration (cyan) was much slower than the new dynamic programming algorithm (pink). In many cases, this is the difference between a brief wait and completely infeasible calculation.

Figure 4.

Example of a flipped active-site histidine found and corrected by Reduce. Top: His 125 of the apo LpxA clashes (red spikes) with nearby Asp 126 rather than H-bonding (green dots), prompting Reduce to suggest flipping it. Bottom: Once the product (gold) was modeled into its electron density (32), it was evident that the flipped position is necessary for His 125 to participate in catalysis.