MolProbity

From Proteopedia

MolProbity^[1][2][3] is a web service for validation of 3D atomic models of macromolecules (protein, RNA, etc) produced by experimental methods such as x-ray crystallography or nuclear magnetic resonance (NMR). Its central feature is "all-atom contact analysis", which adds and optimizes all hydrogen atoms in the Reduce program^[4] and then calculates their H-bond, steric clash, and favorable van der Waals contacts in Probe^[5]. It produces a variety of both global and local numerical scores, and visualizes the individual outliers on the 3D structure - a key to those outlier flags is shown in the figure.