MolProbity - An Active Validation Tool



MolProbity is a web application that integrates validation programs from the Richardson lab at Duke University.


MolProbity provides the user with an expert-system consultation about the accuracy of a macromolecular structure model, diagnosing local problems and enabling their correction. It combines all atom contact analysis with updated versions of more traditional tools for validating geometry and dihedral-angle combinations. MolProbity is most complete for crystal structures of proteins and RNA, but also handles DNA, ligands, and NMR ensembles. It works best as an active validation tool - used as soon as a model is available and during each rebuild/refine loop, not just at the end to provide global statistics before deposition. It produces coordinates, graphics, and numerical evaluations that integrate with either manual or automated use in systems such as PHENIX, KiNG, or Coot.


The integrated MolProbity web application is at The user is guided through a work-flow that typically consists of:

An increasingly broad subset of MolProbity functionalities are integrated directly into PHENIX for use in refinement, Resolve, and wizard decisions. These are all available in the PHENIX GUI as part of the `comprehensive validation interface `_, which runs all available analyses and provides convenient links to molecular graphics software. Phenix.reduce provides optimized hydrogen addition, phenix.probe and provide all-atom clash analysis, and python versions of the Ramachandran and rotamer scores are available in the mmtbx. Interactive all-atom contact dots are also available in Coot.

Possible Problems

Web usage requires Java, Javascript, and a modern web browser.

MolProbity provides reasonable session protection, but if security or large-scale usage are at issue, you can install MP to run on your own Linux or Mac computer provided that the computer has a web server (Apache), the PHP scripting language, JAVA, and a few common Unix utility programs. For more information, follow the "Download MolProbity" link on the MP main page.