EMDataBank Project Team

1. EMDataBank Project Team Baylor College of Medicine Wah Chiu*, PI Grigore Pintilie* Matthew Baker* Matthew Dougherty Steven Ludtke Rutgers University Helen Berman, co-PI Catherine Lawson* Raul Sala* Brian Hudson John Westbrook European Bioinformatics Institute Gerard Kleywegt, co-PI Eduardo Sanz Garcia* Matthew Conroy* Ingvar Lagerstedt Ardan Patwardhan *supported by NIH R01GM079429

2. Establish and maintain 3DEM data standards Create integrated deposition systems Create single archival repository for maps, models and metadata Provide web-based access tools to deliver and manage maps, models and metadata Assess and develop tools needed for map and model validation EMDataBank Mission (2007-12)

3. EM Validation Task Force • Charge: advise on approaches to validate EM maps and map-derived models • Sept 28-29, 2010 meeting • Day 1: plenary presentations • Day 2: separate Map and Model group meetings to discuss specific issues Co-chairs: Richard Henderson Andrej Sali

4. Maps Richard Henderson-Chair (MRC) Bridget Carragher (Scripps) Ken Downing (LBL) Edward Egelman (U Virginia) Joachim Frank (Columbia) Niko Grigorieff (Brandeis) Wen Jiang (Purdue) Steven Ludtke (Baylor) Ohad Medalia (Ben Gurion) Pawel A. Penczek (UT Houston) Michael Schmid (Baylor) Alasdair Steven (NIH) EM VTF Members • Models • Andrej Sali-Chair (UCSF) • Matthew Baker (Baylor) • Peter Rosenthal (NIMR) • Michael G. Rossmann (Purdue) • Gunnar Schroeder (FZ Juelich) • Willy Wriggers (DE Shaw)

5. General Recommendations • Journals should encourage map and/or model deposition before publication • A set of guidelines for what should be included with the publication of a 3DEM structure should be established and shared with journal editors • Maps and models that have been peer reviewed and referred to in published literature should be publicly available • EMDataBank can play a key role • Provide unified access to 3DEM molecular models and their annotations • Support development of data standards to facilitate exchange of information and algorithms • User interface should allow a broad range of queries

6. Map Recommendations - 1 • Standards for assessing map resolution and accuracy need to be developed • No widely accepted validation methods to assess map accuracy • EMDataBank can provide table of existing map-validation techniques • Resolution should be reported and visible structural features should be in accordance with the claimed resolution • Full FSC curve to Nyquist frequency, map manipulations and transformations as well as key parameters of reconstruction algorithms should be reported • Map symmetry should be validated

7. Map Recommendations - 2 • Depositions should include annotations specific to each map type • 2D crystal*, helical*, single particle, tomogram, sub-tomogram average (*may use single-particle methodology) • The requirements and practicalities for archiving raw image data should be investigated • Benchmark raw image data should be made available for methods development

8. Model Recommendations I • Criteria for assessing models must be established • Methods are being developed, no dominant ones have emerged • Three assessment types: • without regard to the 3DEM map: use X-ray VTF criteria • with regard to the 3DEM map: composite scores, correlation coefficients, real-space fit values • with regard to additional data not used in modelling, e.g. cross-linking, antibody labels, spectroscopic measurements

9. Model Recommendations II • Community-wide benchmarks for modelling methods need to be created • Capability to archive coarse-grained representations of models is needed • Sequences of all components need to be annotated