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NMPDR - National Microbial Pathogen Data Resource

NAR Molecular Biology Database Collection entry number 1040
Overbeek, Ross; Olson, Robert; Pusch, Gordon; Olsen, Gary; Davis, James; Disz, Terry; Edwards, Robert; Gerdes, Svetlana; Parrello, Bruce; Shukla, Maulik; Vonstein, Veronika; Wattam, Alice; Xia, Fangfang; Stevens, Rick
1Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA
2Computation Institute, University of Chicago, Chicago, IL 60637, USA
3Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
4Department of Microbiology and Immunology, College of Pharmacy, Cairo University, Cairo, Egypt
5San Diego State University, San Diego, CA 92182, USA
6Burnham Institute for Medical Research, La Jolla, CA 92037, USA
7National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
8Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA

Database Description

The National Microbial Pathogen Data Resource ( is one of eight Bioinformatics Resource Centers funded by the National Institute of Allergy and Infectious Disease (NIAID) to provide a comprehensive bioinformatics environment to support research in biodefense, emerging and re-emerging pathogens. NMPDR is both a central repository for a wide variety of scientific data on Priority Category B pathogenic microorganisms and a platform for software tools that support investigator-driven data analysis. NMPDR curators annotate genomes vertically by developing subsystems, which provide researchers with corrected functional annotations in a structured biological context. The database includes all essentially complete, public genomes to provide a rich context for comparative analysis.

Recent Developments

A growing library of candidate targets for therapeutic intervention, both vaccines and drugs, is being generated from NMPDR sequence data, curated literature annotations, and structural data from Protein Data Bank (PDB). In silico screening is performed for about 70 of the proposed drug targets annually. Results of the computational docking are provided as it becomes available.


This project has been funded in whole or in part with Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract No. HHSN266200400042C.


1. Overbeek R., Begley T., Butler R.M., Choudhuri J.V., Chuang H.Y., Cohoon M., de Crecy-Lagard V., Diaz N., Disz T., Edwards R. et al. (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res., 33, 5691-5702.
2. Overbeek R. et al. (2007) The National Microbial Pathogen Database Resource (NMPDR): A genomics platform based on subsystem annotation. Nucleic Acids Res. 35: in press

Go to the abstract in the NAR 2014 Database Issue.
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