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The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data

H. Berman, K. Henrick, H. Nakamura, J. L. Markley
2007 Nucleic Acids Research  
The worldwide Protein Data Bank (wwPDB) is the international collaboration that manages the deposition, processing and distribution of the PDB archive.  ...  The mission of the wwPDB is to maintain a single archive of macromolecular structural data that are freely and publicly available to the global community.  ...  ACKNOWLEDGEMENTS The RCSB PDB is operated by Rutgers, The State University of New Jersey and the San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University  ... 
doi:10.1093/nar/gkl971 pmid:17142228 pmcid:PMC1669775 fatcat:bukrvoz4dfdgda3vsb4df4rkgy

Announcing the worldwide Protein Data Bank

Helen Berman, Kim Henrick, Haruki Nakamura
2003 Nature Structural & Molecular Biology  
ACKNOWLEDGMENTS The RCSB PDB is supported by funds from the National Science Foundation, the Department of Energy, and the National Institutes of Health.  ...  PDBj is supported by grant-in-aid from the Institute for Bioinformatics Research and Development, Japan Science and Technology Corporation (BIRD-JST), and the Ministry of Education, Culture, Sports, Science  ...  The creation of the wwPDB formalizes the international character of the PDB and ensures that the archive remains single and uniform.  ... 
doi:10.1038/nsb1203-980 pmid:14634627 fatcat:24q3n52d6jdunlogzle6x6bab4

The wwPDB remediation project

G. J. Swaminathan, B. Schneider
2007 Acta Crystallographica Section A Foundations of Crystallography  
, rheumatoid arthritis) [ The worldwide Protein Data Bank (wwPDB) [1] , [2] is a group of organizations that act as data centres for deposition, processing and distribution of data in the Protein  ...  Data Bank (PDB) [3] .  ... 
doi:10.1107/s0108767307099497 fatcat:jaobgr6wcrexnbd7kf3dnurv4q

Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data

Jasmine Y Young, John D Westbrook, Zukang Feng, Ezra Peisach, Irina Persikova, Raul Sala, Sanchayita Sen, John M Berrisford, G Jawahar Swaminathan, Thomas J Oldfield, Aleksandras Gutmanas, Reiko Igarashi (+39 others)
2018 Database: The Journal of Biological Databases and Curation  
Abstract The Protein Data Bank (PDB) is the single global repository for experimentally determined 3D structures of biological macromolecules and their complexes with ligands.  ...  Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data.  ...  Acknowledgements The authors thank all the members of the worldwide Protein Data Bank (wwPDB) for their support and feedback, Kim Henrick for his direction to the PDB in Europe (PDBe) biocuration team  ... 
doi:10.1093/database/bay002 pmid:29688351 pmcid:PMC5804564 fatcat:pymncvy65zghjgdhleavnz7oce

OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive

Jasmine Y. Young, John D. Westbrook, Zukang Feng, Raul Sala, Ezra Peisach, Thomas J. Oldfield, Sanchayita Sen, Aleksandras Gutmanas, David R. Armstrong, John M. Berrisford, Li Chen, Minyu Chen (+37 others)
2017 Structure  
by the worldwide PDB (wwPDB) partners.  ...  This new system was designed to ensure that the wwPDB could meet the evolving archiving requirements of the scientific community over the coming decades.  ...  ACKNOWLEDGEMENTS The authors thank all the members of Worldwide PDB for their support and feedback, especially Kumaran Baskaran, Toshimichi Fujiwara, Takeshi  ... 
doi:10.1016/j.str.2017.01.004 pmid:28190782 pmcid:PMC5360273 fatcat:okamctypwvdrxfomgjio4rsvma

The future of the protein data bank

Helen M. Berman, Gerard J. Kleywegt, Haruki Nakamura, John L. Markley
2012 Biopolymers  
The Worldwide Protein Data Bank (wwPDB) is the international collaboration that manages the deposition, processing and distribution of the PDB archive.  ...  The wwPDB's mission is to maintain a single archive of macromolecular structural data that are freely and publicly available to the global community.  ...  The archive is managed by the Worldwide Protein Data Bank organization (wwPDB), whose mission is to ensure that a single, global PDB data archive is and will remain freely and publicly available. 3 The  ... 
doi:10.1002/bip.22132 pmid:23023942 pmcid:PMC3684242 fatcat:tkdo6ykibnhebfbavqjb55nhsq

The Protein Data Bank archive as an open data resource

Helen M. Berman, Gerard J. Kleywegt, Haruki Nakamura, John L. Markley
2014 Journal of Computer-Aided Molecular Design  
The Protein Data Bank archive was established in 1971, and recently celebrated its 40th anniversary (Berman et al. in Structure 20:391, 2012).  ...  An analysis of interrelationships of the science, technology and community leads to further insights into how this resource evolved into one of the oldest and most widely used open-access data resources  ...  Acknowledgments The wwPDB thanks all staff members past and present, and all members of the PDB community.  ... 
doi:10.1007/s10822-014-9770-y pmid:25062767 pmcid:PMC4196035 fatcat:yhd3biuk5relpdwfijmmiliyk4

How Community Has Shaped the Protein Data Bank

Helen M. Berman, Gerard J. Kleywegt, Haruki Nakamura, John L. Markley
2013 Structure  
Following several years of community discussion, the Protein Data Bank (PDB) was established in 1971 as a public repository for the coordinates of three-dimensional models of biological macromolecules.  ...  Over the last 40 years, the Protein Data Bank (PDB) has grown from a small data repository promoted by the structural biology community to a critical international resource used around the world in a broad  ...  ACKNOWLEDGMENTS The wwPDB thanks staff past and present and all members of the PDB community.  ... 
doi:10.1016/j.str.2013.07.010 pmid:24010707 pmcid:PMC4435976 fatcat:ifkxbpcv35eoln3w34jgxmymfq

Establishing the Next Generation of the Protein Data Bank

Helen Berman
2014 The Winnover  
ACKNOWLEDGEMENTS The RCSB PDB is funded by the NSF (DBI 0829586 ), NIH, and DOE. RCSB PDB is a member of the Worldwide Protein Data Bank.  ...  These partnerships were formalized in 2003 with the creation of the Worldwide Protein Data Bank (wwPDB; wwpdb.org), whose new mission was to ensure standard representation and processing standards in the  ...  A goal of the RCSB PDB is to create a structural view of biology. That goal is within reach.  Establishing the Next Generation of the Protein Data Bank Berman, H.M., J. Westbrook, Z. Feng, G.  ... 
doi:10.15200/winn.140076.68556 fatcat:skuxt46q2ngvjgh5r3tzfklxju

Is there a Sevres standard for protein structures?

A. Wlodawer, M. Jaskolski, Z. Dauter
2007 Acta Crystallographica Section A Foundations of Crystallography  
The availability in the PDB of a number of protein models refined at ultrahigh resolution offers the possibility of creating a library of protein geometry built on most accurately refined protein models  ...  Limited resolution of the diffraction data collected for most of protein crystals do not allow their models to be refined without introduction of stereochemical restraints.  ...  MS07 O4 The wwPDB remediation project Ganesh The worldwide Protein Data Bank (wwPDB) [1] , [2] is a group of organizations that act as data centres for deposition, processing and distribution of  ... 
doi:10.1107/s0108767307099527 fatcat:wi3y5qwpjjetppd75orkvadc5m

Improvement of crystallographic data near corners in mosaic CCD detectors

A. S. Arvai, S. Brockhauser, G. Cioci, G. A. Leonard, A. McCarthy, S. McSweeney, C. Müller-Diekmann, C. Nielsen, D. Nurizzo, R. B. G. Ravelli, X. Nguyen-huu
2007 Acta Crystallographica Section A Foundations of Crystallography  
The availability in the PDB of a number of protein models refined at ultrahigh resolution offers the possibility of creating a library of protein geometry built on most accurately refined protein models  ...  Limited resolution of the diffraction data collected for most of protein crystals do not allow their models to be refined without introduction of stereochemical restraints.  ...  MS07 O4 The wwPDB remediation project Ganesh The worldwide Protein Data Bank (wwPDB) [1] , [2] is a group of organizations that act as data centres for deposition, processing and distribution of  ... 
doi:10.1107/s0108767307099515 fatcat:3tfihrjo4zg5zgrng6mrvzcqb4

Tandem use of crystallography and mass spectrometry to sequenceab initioHPBP

E. Chabriere, M. Elias, H. Diemer, F. Renault, C. Contreras-Martel, A. Van Dorsselaer
2007 Acta Crystallographica Section A Foundations of Crystallography  
The availability in the PDB of a number of protein models refined at ultrahigh resolution offers the possibility of creating a library of protein geometry built on most accurately refined protein models  ...  Limited resolution of the diffraction data collected for most of protein crystals do not allow their models to be refined without introduction of stereochemical restraints.  ...  MS07 O4 The wwPDB remediation project Ganesh The worldwide Protein Data Bank (wwPDB) [1] , [2] is a group of organizations that act as data centres for deposition, processing and distribution of  ... 
doi:10.1107/s0108767307099503 fatcat:owqaapy6cbd5hdtjpyxfvoukha

The Protein Data Bank: a historical perspective

Helen M. Berman
2007 Acta Crystallographica Section A Foundations of Crystallography  
The Protein Data Bank began as a grassroots effort in 1971.  ...  The interplay of science, technology and attitudes about data sharing have all played a role in the growth of this resource.  ...  The history of the Protein Data Bank The establishment of the Protein Data Bank (PDB) began in the 1970's as a grassroots effort.  ... 
doi:10.1107/s0108767307035623 pmid:18156675 fatcat:75muama2a5fjne52mkampxpcpm

Worldwide Protein Data Bank validation information: usage and trends

Oliver S. Smart, Vladimír Horský, Swanand Gore, Radka Svobodová Vařeková, Veronika Bendová, Gerard J. Kleywegt, Sameer Velankar
2018 Acta Crystallographica Section D: Structural Biology  
Realising the importance of assessing the quality of the biomolecular structures deposited in the Protein Data Bank (PDB), the Worldwide Protein Data Bank (wwPDB) partners established Validation Task Forces  ...  The ValTrendsDB database provides users with a convenient way to access and analyse validation information and other properties of X-ray crystal structures in the PDB, including investigating trends in  ...  We would like to thank all of the wwPDB partners, the OneDep team, the wwPDB X-ray VTF members and the authors of the software packages used in the wwPDB validation pipeline for their advice.  ... 
doi:10.1107/s2059798318003303 pmid:29533231 pmcid:PMC5947764 fatcat:cv2p2rg53ffkfo7annzz5gloky

Creating a community resource for protein science

Helen M. Berman
2012 Protein Science  
a resource for protein science and to try to quantify the impact of having PDB data openly available.  ...  This award and the 40th anniversary of the Protein Data Bank (PDB; Berman et al., Structure 2012;20:391-396) have given me an opportunity to reflect on the various components that have contributed to building  ...  Acknowledgments Many people at the wwPDB data centers support the continued viability and quality of the PDB archive, in particular that of the leaders of the member sites Kim Henrick, Gerard Kleywegt,  ... 
doi:10.1002/pro.2154 pmid:22969036 pmcid:PMC3527698 fatcat:f7xzqqfwajbntkt6jz3p3t3cjy
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