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

By Ian W Davis, Andrew Leaver-Fay, Vincent B. Chen, Jeremy N. Block, Gary J. Kapral, Xueyi Wang, L. Murray, W. Bryan, Arendall Iii, Jack Snoeyink and 2 more. 2007

3,833 citations recorded by the source corpus.

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.

Subfields: Materials Chemistry, Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

1. Paul D. Adams
2. David Baker
3. Randy J. Read
4. Pavel V. Afonine
5. Yang Zhang
6. T. C. Terwilliger
7. Andriy Kryshtafovych
8. Nigel W. Moriarty

In Molecular Biology

1. David Baker
2. Yang Zhang
3. Randy J. Read
4. Paul D. Adams
5. Rhiju Das
6. Andriy Kryshtafovych
7. Torsten Schwede
8. T. C. Terwilliger

Citations in the corpus

• Assessment of three-dimensional RNA structure prediction in CASP15 (2023, positive): “…stereochemical violations); and (5) PHENIX, which reports a clashscore metric for all non-hydrogen bonded atom pairs that overlap worse than 0.4 Å. 26,37 For TM-score and GDT_TS, super-position of models and experimental models were calculated with default atoms for those packages, C3 0 and C4 0…”
• Towards automated crystallographic structure refinement with phenix.refine (2012, methodology): “A comprehensive suite of validation tools largely derived from MolProbity (Davis et al., 2007; Chen et al., 2010) is run as the final step of refinement and these analyses are integrated into the display of results.”
• Features and development of Coot (2010, neutral): “It also provides convenient interfaces to external validation tools: most notably the MolProbity suite (Davis et al. , 2007), but also to the REFMAC refinement software (Murshudov et al. , 1997) and dictionary (Vagin et al. , 2004).”
• High resolution comparative modeling with RosettaCM (2013, methodology): “Overall stereochemical quality – as reported by the Molprobity score(Davis et al., 2007) – was also highest for the RosettaServer models.”
• Structural and immunologic characterization of bovine, horse, and rabbit serum albumins (2012, methodology): “Validation of the structures was performed using MOLPROBITY (Davis et al., 2007) and ADIT (Yang et al.”
• Tight and specific lanthanide binding in a de novo TIM barrel with a large internal cavity designed by symmetric domain fusion (2020, positive): “The model quality was validated using MolProbity (46).”
• Low-resolution refinement tools in REFMAC5 (2012, methodology): “Model validation (geometry and contact analysis) was performed using the MolProbity server (Chen et al., 2010; Davis et al., 2007).”
• Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank (2011, methodology): “PDB entries deposited before 1983, and for which the experimental data were available, were selected and sorted by deposition date.”
• RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures (2015, methodology): “Clash Score as computed by the MolProbity suite (Davis et al. 2007).”
• MolProbity: all-atom structure validation for macromolecular crystallography (2009, neutral): “Summary of MolProbity flow and user interactions The usual interaction with MolProbity (Davis et al., 2007) is through the internet at http://molprobity.biochem.duke.edu or as a main menu item on our general laboratory website at http://kinemage.biochem.duke.edu.”
• Conformation Dependence of Backbone Geometry in Proteins (2009, methodology): “To understand the structural basis of variations between these theoretical peptides, van der Waals clashes were visually analyzed using the Coot (Emsley and Cowtan, 2004) interface to MolProbity (Davis et al., 2007).”