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Title: Remediation of the protein data bank archive

Abstract

The Worldwide Protein Data Bank (wwPDB; wwpdb. org) is the international collaboration that manages the deposition, processing and distribution of the PDB archive. The online PDB archive at ftp:// ftp.wwpdb.org is the repository for the coordinates and related information for more than 47 000 structures, including proteins, nucleic acids and large macromolecular complexes that have been determined using X-ray crystallography, NMR and electron microscopy techniques. The members of the wwPDB–RCSB PDB (USA), MSD-EBI (Europe), PDBj (Japan) and BMRB (USA)–have remediated this archive to address inconsistencies that have been introduced over the years. The scope and methods used in this project are presented.

Authors:
 [1];  [2];  [3];  [1];  [4];  [2];  [2];  [1];  [5];  [1];  [2];  [4];  [5];  [1];  [5];  [1];  [1];  [2];  [4];  [1] more »;  [2];  [5];  [2];  [2];  [2];  [2] « less
+ Show Author Affiliations
  1. European Molecular Biology Lab. (EMBL), Hinxton, Cambridge (United Kingdom). MSD-EBI
  2. Rutgers Univ., Piscataway, NJ (United States). Dept. of Chemistry and Chemical Biology. RCSB Protein Data Bank
  3. Univ. of California, San Diego, CA (United States). The Skaggs School of Pharmacy and Pharmaceutical Sciences. San Diego Supercomputer Center. RCSB Protein Data Bank
  4. Univ. of Wisconsin, Madison, WI (United States). Dept. of Biochemistry. BioMagResBank
  5. Osaka Univ. (Japan). Inst. for Protein Research. PDBj
Publication Date:
Research Org.:
Rutgers Univ., Piscataway, NJ (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division; National Institutes of Health (NIH); National Science Foundation (NSF)
OSTI Identifier:
1625433
Grant/Contract Number:  
LM05799; DBI 03-12718
Resource Type:
Accepted Manuscript
Journal Name:
Nucleic Acids Research
Additional Journal Information:
Journal Volume: 36; Journal Issue: suppl_1; Journal ID: ISSN 0305-1048
Publisher:
Oxford University Press
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Biochemistry & Molecular Biology

Citation Formats

Henrick, K., Feng, Z., Bluhm, W. F., Dimitropoulos, D., Doreleijers, J. F., Dutta, S., Flippen-Anderson, J. L., Ionides, J., Kamada, C., Krissinel, E., Lawson, C. L., Markley, J. L., Nakamura, H., Newman, R., Shimizu, Y., Swaminathan, J., Velankar, S., Ory, J., Ulrich, E. L., Vranken, W., Westbrook, J., Yamashita, R., Yang, H., Young, J., Yousufuddin, M., and Berman, H. M. Remediation of the protein data bank archive. United States: N. p., 2007. Web. doi:10.1093/nar/gkm937.
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Henrick, K., Feng, Z., Bluhm, W. F., Dimitropoulos, D., Doreleijers, J. F., Dutta, S., Flippen-Anderson, J. L., Ionides, J., Kamada, C., Krissinel, E., Lawson, C. L., Markley, J. L., Nakamura, H., Newman, R., Shimizu, Y., Swaminathan, J., Velankar, S., Ory, J., Ulrich, E. L., Vranken, W., Westbrook, J., Yamashita, R., Yang, H., Young, J., Yousufuddin, M., & Berman, H. M. Remediation of the protein data bank archive. United States. https://doi.org/10.1093/nar/gkm937
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Henrick, K., Feng, Z., Bluhm, W. F., Dimitropoulos, D., Doreleijers, J. F., Dutta, S., Flippen-Anderson, J. L., Ionides, J., Kamada, C., Krissinel, E., Lawson, C. L., Markley, J. L., Nakamura, H., Newman, R., Shimizu, Y., Swaminathan, J., Velankar, S., Ory, J., Ulrich, E. L., Vranken, W., Westbrook, J., Yamashita, R., Yang, H., Young, J., Yousufuddin, M., and Berman, H. M. Tue . "Remediation of the protein data bank archive". United States. https://doi.org/10.1093/nar/gkm937. https://www.osti.gov/servlets/purl/1625433.
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@article{osti_1625433,
title = {Remediation of the protein data bank archive},
author = {Henrick, K. and Feng, Z. and Bluhm, W. F. and Dimitropoulos, D. and Doreleijers, J. F. and Dutta, S. and Flippen-Anderson, J. L. and Ionides, J. and Kamada, C. and Krissinel, E. and Lawson, C. L. and Markley, J. L. and Nakamura, H. and Newman, R. and Shimizu, Y. and Swaminathan, J. and Velankar, S. and Ory, J. and Ulrich, E. L. and Vranken, W. and Westbrook, J. and Yamashita, R. and Yang, H. and Young, J. and Yousufuddin, M. and Berman, H. M.},
abstractNote = {The Worldwide Protein Data Bank (wwPDB; wwpdb. org) is the international collaboration that manages the deposition, processing and distribution of the PDB archive. The online PDB archive at ftp:// ftp.wwpdb.org is the repository for the coordinates and related information for more than 47 000 structures, including proteins, nucleic acids and large macromolecular complexes that have been determined using X-ray crystallography, NMR and electron microscopy techniques. The members of the wwPDB–RCSB PDB (USA), MSD-EBI (Europe), PDBj (Japan) and BMRB (USA)–have remediated this archive to address inconsistencies that have been introduced over the years. The scope and methods used in this project are presented.},
doi = {10.1093/nar/gkm937},
journal = {Nucleic Acids Research},
number = suppl_1,
volume = 36,
place = {United States},
year = {Tue Dec 11 00:00:00 EST 2007},
month = {Tue Dec 11 00:00:00 EST 2007}
}
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