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

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124 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

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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.",

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",

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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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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

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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.

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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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