# Unified Data Resource for 3DEM

> **NIH NIH R01** · STANFORD UNIVERSITY · 2021 · $624,425

## Abstract

Abstract
Three-dimensional transmission electron microscopy (3DEM) has become a cutting-edge method for
determining structures of large biological assemblies due to recent technical advances. Hundreds of 3DEM
experiments are reported in the literature each year and more than 4400 structures are now available in public
archives through our EMDataBank.org website. Since 2014, following the cryo-electron microscopy "resolution
revolution," more than 500 maps with resolutions better than 5.0 Å have been released, most with associated
coordinate models. It is critically important that 3DEM maps and the models derived from them are of the
highest possible quality, and to achieve this aim it is necessary to have community-accepted validation
measures. In our current funding period we developed and promoted new methods and infrastructure to
determine map accuracy and resolution, as well as novel methods to build and validate map-derived models.
In addition, we hosted challenges and meetings to involve the 3DEM and modeling communities in developing
new map and model validation standards. We also significantly expanded the underlying representation for
3DEM experimental methods, and collaborated to fully integrate 3DEM into the wwPDB Deposition and
Annotation system. We propose here to continue to develop innovative solutions for validating 3DEM-derived
structures of macromolecular assemblies, focusing on the moderate to high resolution range, 5-2 Å. To
achieve this we will host new challenges formulated to engage the community using increasingly complex data
derived by 3DEM methods and provide statistical analysis of their outcomes. In addition, we will develop and
evaluate computational protocols that yield quantifiable parameters for validating 3DEM-derived structures, in
terms of density map resolvability, map and model correlation and atom position uncertainty of the associated
model. We will also improve the validation criteria for nucleic acids, which occur in 30% of all 3DEM derived
models. We will use the EMDataBank website to disseminate the results of our investigations and to provide a
platform for community engagement and discussions. Our approach will continue to build on the decades of
experience of our team in developing tools for 3DEM map generation and modeling, analyzing large
assemblies especially those containing nucleic acids, and working with the community to create standards for
structure validation.

## Key facts

- **NIH application ID:** 10092169
- **Project number:** 5R01GM079429-13
- **Recipient organization:** STANFORD UNIVERSITY
- **Principal Investigator:** Wah Chiu
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $624,425
- **Award type:** 5
- **Project period:** 2007-08-15 → 2022-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10092169

## Citation

> US National Institutes of Health, RePORTER application 10092169, Unified Data Resource for 3DEM (5R01GM079429-13). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10092169. Licensed CC0.

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