2024-07-17 : 37051 EMDB map entries, 21507 PDB coordinate entries RCSB PDB | PDBe

A vision for validation of 3DEM maps and map-derived models

We are pleased to announce the publication of the outcome of the first Electron Microscopy Validation Task Force (EM VTF) meeting in the journal Structure: Henderson et al., Structure (2012).

The inaugural meeting of the EM VTF, organized by Unified Data Resource for 3DEM, was held at Rutgers University in New Brunswick, NJ on September 28 and 29, 2010. An international group of 3DEM experts explored how to assess maps, models, and other data that are deposited into the EM Data Bank (EMDB) and Protein Data Bank (PDB) public data archives. The 2-day workshop was co-chaired by Richard Henderson (MRC, Cambridge) and Andrej Sali (UCSF).

For deposited maps, the EM VTF recognized a critical need to develop standards for assessing map resolution and accuracy, and recommended reporting of map resolution in accordance with visible features, deposition of annotations specific to each map type, and validation of map symmetry.

For deposited map-derived models, EM VTF recommendations include establishment of criteria for assessing models both with and without regard to the fit to the map, creation of community-wide benchmarks for modelling methods, sequence annotation of all map components, and capability to archive coarse-grained representations of models.

Additional recommendations include establishing deposition guidelines for publication of 3DEM structures in journals, and expanding the role of our project to work together with the 3DEM community to provide unified access to 3DEM structures and to facilitate development of validation and data standards.

This initial report by the EM VTF follows closely on the heels of recommendations by the wwPDB X-ray VTF published last year (Structure, 2011 19: 1395-1412). Additional task forces have been convened for NMR and small angle scattering methods.

The efforts of all of the report authors are greatly appreciated: Richard Henderson, Andrej Sali, Matthew L. Baker, Bridget Carragher, Batsal Devkota, Kenneth H. Downing, Edward H. Egelman, Zukang Feng, Joachim Frank, Nikolaus Grigorieff, Wen Jiang, Steven J. Ludtke, Ohad Medalia, Pawel A. Penczek, Peter B. Rosenthal, Michael G. Rossmann, Michael F. Schmid, Gunnar F. Schröder, Alasdair C. Steven, David L. Stokes, John D. Westbrook, Willy Wriggers, Huanwang Yang, Jasmine Young, Helen M. Berman, Wah Chiu, Gerard J. Kleywegt, and Catherine L. Lawson.

The Unified Data Resource for 3DEM was established in 2007 and is a joint effort of the Protein Data Bank in Europe (PDBe) at the European Bioinformatics Institute, the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) at Rutgers, and the National Center for Macromolecular Imaging (NCMI) at Baylor College of Medicine, and is funded by the National Institutes of Health. The project serves the 3DEM and wider scientific communities with its 3DEM-specific portal for deposition and access to EM-derived structures and links to software, validation standards and conventions. The new report will serve as our roadmap for development of validation standards for data in 3DEM public data archives in collaboration with the 3DEM community.

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