Remediation of the protein data bank archive

Kim Henrick; Zukang Feng; Wolfgang F. Bluhm; Dimitris Dimitropoulos; Jurgen F. Doreleijers; Shuchismita Dutta; Judith L. Flippen-Anderson; John Ionides; Chisa Kamada; Eugene Krissinel; Catherine L. Lawson; John L. Markley; Haruki Nakamura; Richard Newman; Yukiko Shimizu; Jawahar Swaminathan; Sameer Velankar; Jeramia Ory; Eldon L. Ulrich; Wim Vranken; John Westbrook; Reiko Yamashita; Huanwang Yang; Jasmine Young; Muhammed Yousufuddin; Helen M. Berman

doi:10.1093/nar/gkm937

Remediation of the protein data bank archive

Kim Henrick
, Zukang Feng
, Wolfgang F. Bluhm
, Dimitris Dimitropoulos
, Jurgen F. Doreleijers
, Shuchismita Dutta
, Judith L. Flippen-Anderson
, John Ionides
, Chisa Kamada
, Eugene Krissinel
, Catherine L. Lawson
, John L. Markley
, Haruki Nakamura
, Richard Newman
, Yukiko Shimizu
, Jawahar Swaminathan
, Sameer Velankar
, Jeramia Ory
, Eldon L. Ulrich
, Wim Vranken

John Westbrook, Reiko Yamashita, Huanwang Yang, Jasmine Young, Muhammed Yousufuddin, Helen M. Berman

Research output: Contribution to journal › Article › peer-review

125 Scopus citations

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.

Original language	English
Pages (from-to)	D426-D433
Journal	Nucleic acids research
Volume	36
Issue number	SUPPL. 1
DOIs	https://doi.org/10.1093/nar/gkm937
State	Published - Jan 2008

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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., ... Berman, H. M. (2008). Remediation of the protein data bank archive. Nucleic acids research, 36(SUPPL. 1), D426-D433. https://doi.org/10.1093/nar/gkm937

@article{83cb7eefc5984a6091d27a68c9ac5600,

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.",

author = "Kim Henrick and Zukang Feng and Bluhm, \{Wolfgang F.\} and Dimitris Dimitropoulos and Doreleijers, \{Jurgen F.\} and Shuchismita Dutta and Flippen-Anderson, \{Judith L.\} and John Ionides and Chisa Kamada and Eugene Krissinel and Lawson, \{Catherine L.\} and Markley, \{John L.\} and Haruki Nakamura and Richard Newman and Yukiko Shimizu and Jawahar Swaminathan and Sameer Velankar and Jeramia Ory and Ulrich, \{Eldon L.\} and Wim Vranken and John Westbrook and Reiko Yamashita and Huanwang Yang and Jasmine Young and Muhammed Yousufuddin and Berman, \{Helen M.\}",

year = "2008",

month = jan,

doi = "10.1093/nar/gkm937",

language = "English",

volume = "36",

pages = "D426--D433",

journal = "Nucleic acids research",

issn = "0305-1048",

number = "SUPPL. 1",

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Henrick, K, Feng, Z, Bluhm, WF, Dimitropoulos, D, Doreleijers, JF, Dutta, S, Flippen-Anderson, JL, Ionides, J, Kamada, C, Krissinel, E, Lawson, CL, Markley, JL, Nakamura, H, Newman, R, Shimizu, Y, Swaminathan, J, Velankar, S, Ory, J, Ulrich, EL, Vranken, W, Westbrook, J, Yamashita, R, Yang, H, Young, J, Yousufuddin, M & Berman, HM 2008, 'Remediation of the protein data bank archive', Nucleic acids research, vol. 36, no. SUPPL. 1, pp. D426-D433. https://doi.org/10.1093/nar/gkm937

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T1 - Remediation of the protein data bank archive

AU - Henrick, Kim

AU - Feng, Zukang

AU - Bluhm, Wolfgang F.

AU - Dimitropoulos, Dimitris

AU - Doreleijers, Jurgen F.

AU - Dutta, Shuchismita

AU - Flippen-Anderson, Judith L.

AU - Ionides, John

AU - Kamada, Chisa

AU - Krissinel, Eugene

AU - Lawson, Catherine L.

AU - Markley, John L.

AU - Nakamura, Haruki

AU - Newman, Richard

AU - Shimizu, Yukiko

AU - Swaminathan, Jawahar

AU - Velankar, Sameer

AU - Ory, Jeramia

AU - Ulrich, Eldon L.

AU - Vranken, Wim

AU - Westbrook, John

AU - Yamashita, Reiko

AU - Yang, Huanwang

AU - Young, Jasmine

AU - Yousufuddin, Muhammed

AU - Berman, Helen M.

PY - 2008/1

Y1 - 2008/1

N2 - 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.

AB - 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.

UR - https://www.scopus.com/pages/publications/38549176153

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DO - 10.1093/nar/gkm937

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SN - 0305-1048

VL - 36

SP - D426-D433

JO - Nucleic acids research

JF - Nucleic acids research

IS - SUPPL. 1

ER -

Remediation of the protein data bank archive

Abstract

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