Cryo-electron microscopy (cryoEM) is a maturing methodology in structural biology that enables the determination of 3D structures of macromolecular complexes and cells at a broad range of resolution from 2 to 100 A with information that bridges the gap between cell biology and crystallography/NMR. It is now well accepted by structural, molecular and cell biologists that a cryoEM map and its associated model can form the basis for subsequent hypothesis-driven research and knowledge discovery. In the past four years, several independent workshops organized by the European Bioinformatics Institute (EBI) in Hinxton, UK and the Research Collaboratory for Structural Bioinformatics (RCSB) at Rutgers, the State University of New Jersey, Piscataway, NJ, USA, have reached a community consensus that it is time to establish publicly supported, one-stop deposition and retrieval facilities for cryoEM density maps, atomic models and associated metadata. This proposal is a joint effort among investigators of the EBI, RCSB and the National Center for Macromolecular Imaging (NCMI) at Baylor College of Medicine, Houston. These investigators have complementary expertise in archiving density maps (Kim Henrick), archiving coordinates of atomic models (Kim Henrick, Helen Berman), and all aspects of cryoEM technology development, including data collection, map generation, cryoEM map restrained modeling, visualization, segmentation and annotation (Wah Chiu). We propose to integrate the expertise and infrastructure of the three well-established research centers to create a global deposition and retrieval network for cryoEM maps, models and their associated metadata, as well as a web service for a number of software tools for standardized map format conversion, map segmentation and assessment, model assessment, visualization, and data integration. These tools are essential for verification of the deposited data and would also facilitate efficient use of the archived data. We will develop these tools in consultation with the major developers of cryoEM software. Before inclusion in the set of web services, we will evaluate the suitability of these tools for the intended purposes with the map and coordinate data available in the current data resources. We will fully document the usage and limitations of these tools. Moreover, the new, comprehensive cryoEM data resource will be built in a manner that will be straightforward to maintain and extend as the field grows and matures. Finally, an important component activity of this proposed research is to gather community input throughout the entire grant period so that the final system will be designed and implemented at the highest standards to serve the needs of both cryoEM experts and biological end-users.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM079429-05
Application #
8102764
Study Section
Special Emphasis Panel (ZRG1-BCMB-N (90))
Program Officer
Flicker, Paula F
Project Start
2007-08-15
Project End
2013-05-31
Budget Start
2011-06-01
Budget End
2013-05-31
Support Year
5
Fiscal Year
2011
Total Cost
$890,910
Indirect Cost
Name
Baylor College of Medicine
Department
Biochemistry
Type
Schools of Medicine
DUNS #
051113330
City
Houston
State
TX
Country
United States
Zip Code
77030
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