Chapter 21.6 MolProbity: all-atom structure validation for macromolecular crystallography

Crystallography of biological macromolecules

Second Online Edition (2012)

Part 21. Structure validation

  1. V. B. Chen,
  2. W. B. Arendall,
  3. J. J. Headd,
  4. D. A. Keedy,
  5. R. M. Immormino,
  6. G. J. Kapral,
  7. L. W. Murray,
  8. J. S. Richardson,
  9. D. C. Richardson

Published Online: 14 APR 2012

DOI: 10.1107/97809553602060000884

International Tables for Crystallography

International Tables for Crystallography

How to Cite

Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S. and Richardson, D. C. 2012. MolProbity: all-atom structure validation for macromolecular crystallography. International Tables for Crystallography. F:21:21.6:694–701.

Author Information

  1. Department of Biochemistry, Duke University, Durham, NC 27710, USA

Publication History

  1. Published Online: 14 APR 2012


MolProbity is a structure-validation web service that provides broad-spectrum solidly based evaluation of model quality at both the global and local levels for both proteins and nucleic acids. It relies heavily on the power and sensitivity provided by optimized H-atom placement and all-atom contact analysis, complemented by updated versions of covalent-geometry and torsion-angle criteria. Some of the local corrections can be performed automatically in MolProbity and all of the diagnostics are presented in chart and graphical forms that help guide manual rebuilding. X-ray crystallography provides a wealth of biologically important molecular data in the form of atomic three-dimensional structures of proteins, nucleic acids and increasingly large complexes in multiple forms and states. Advances in automation, in everything from crystallization to data collection to phasing to model building to refinement, have made solving a structure using crystallography easier than ever. However, despite these improvements, local errors that can affect biological interpretation are widespread at low resolution and even high-resolution structures nearly all contain at least a few local errors such as Ramachandran outliers, flipped branched protein side chains and incorrect sugar puckers. It is critical both for the crystallographer and for the end user that there are easy and reliable methods to diagnose and correct these sorts of errors in structures. MolProbity is the authors’ contribution to helping solve this problem and this chapter reviews its general capabilities, reports on recent enhancements and usage, and presents evidence that the resulting improvements are now beneficially affecting the global database.


  • all-atom contacts;
  • clashscore;
  • automated correction;
  • KiNG;
  • MolProbity;
  • ribose pucker;
  • Ramachandran plots;
  • side-chain rotamers;
  • model quality;
  • systematic errors;
  • database improvement