Validation

A key mission of EMDataResource is to engage the 3DEM community in activities that encourage develop validation procedures for 3DEM structures. The Electron Microscopy Validation Task Force (EM VTF) met on September 28-29, 2010 at Rutgers University in New Brunswick NJ. The workshop was co-chaired by Richard Henderson (MRC, Cambridge) for map validation and Andrej Sali (UCSF) for model validation. The EM VTF's initial recommendations are published here: Henderson et al (2012), Structure 20, 205-214. We have also hosted map and model challenges with the goal of encouraging development of new assessment procedures. Results are summarized in this 2010 Biopolymers Special Issue and this 2018 Journal of Structural Biology Special Issue.

Compiled below are validation servers that we are aware of that can be used to assess 3DEM Map and Model quality. Please send any corrections/additions to help@emdataresource.org.

Validation Services: Maps

• Fourier Shell Correlation (FSC): Upload two independent half maps, receive the calculated FSC curve in a standardized format for deposition into EMDB, view and download a plot of the FSC curve (example plot). Developed and hosted at PDBe.
• 3DFSC: Provides a quantitative measure of directional resolution anisotropy, as described in Tan et al Nature Methods 2017. Hosted at the Salk Institute (requires login).
• Tilt-Pair: Validate map hand and overall shape for lower resolution maps in which secondary structure features are absent. This server, originally developed by the Rosenthal group (Wasilewski et al J. Struct Biol 2014), has been migrated to PDBe.
• Scipion: Calculate the local resolution of your map using ResMap, Blocres (from Bsoft), and MonoRes (Xmipp). Reference: Mingo et al Protein Science 2017. Hosted at CNB-CSIC (Spain).

Validation Services: Models

• wwPDB Validation: Upload a structure and (optionally) experimental data to generate a wwPDB validation report. Standalone server performs the same validation procedure that is carried out during deposition of structures to the wwPDB OneDep System. Currently, wwPDB 3DEM validation reports (example pdf)provide author-reported resolution as well as information on model stereochemistry, using the same criteria as provided for X-ray and NMR structures. Reference: Gore et al 2017
• Molprobity: Evaluate the quality of an atomic coordinate model. Reference: Chen et al Acta Cryst D 2010. Hosted by the Richardson Lab (Duke U).
• EMRinger: Calculate the EMRinger score for a model built into an EM map. Reference: Barad et al Nature Methods 2015. Hosted by the Fraser Lab (UCSF).
• DNATCO: Assess RNA or DNA structure relative to common di-nucleotide conformers. Reference: Cerny et al., Nucleic Acids Research 2016. Hosted by Jiří Černý and Bohdan Schneider (Czech Acad Sci).

Validation: Released Maps and Models

• Map Visual Analysis (example): EMDB map orthogonal projections and surface views, central slices, density distribution, map volume estimate, rotationally averaged power spectrum, atom inclusion analysis of associated model into map. Reference: Abbott et al 2018. Hosted at EBI/PDBe.
• wwPDB Validation Reports: Model quality statistics. Reference: Gore et al 2017. Available at all wwPDB partner sites.
• Convergence: Models generated using Rosetta from atomic models and EM densities deposited in PDB/EMDB are sorted by Rosetta score, clash score, Ramachandran outliers, and MolProbity score. Reference: Herzik et al bioRxiv 2017. Hosted by the Lander Lab (UCSF).

Validation Software

Search our software list to find validation software for 3DEM structures.