MolProbity Server

Introduction
The MolProbity server, developed by the Richardson group (Ref. 1,2), is a site for the evaluation of single X-ray structures and NMR structure ensembles.  The server performs a number of validations including all-residue Ramachandran analysis, rotamer analysis, and all-atom clash analysis.  Like the PSVS server, the MolProbity server is a valuable structure validation tool in the final stages of structure refinement.  Structures and various metrics are visualized in the KiNG tool, and all analyses and “kinemages” can be downloaded. 

Using MolProbity server
1.    Uploading a PDB.
PDB files are quickly uploaded, and in the case of NMR ensembles, divided into individual PDB files.  One next analyzes all-atom contacts and geometry (Figure 1).  There is also an “add hydrogens” tool for X-ray structures, which is useful for comparison of NMR/X-ray structure pairs.
Figure 1