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The PDB data uniformity project

T. N. Bhat
2001 Nucleic Acids Research  
This paper describes the data uniformity project that is underway to address the inconsistency in PDB data.  ...  The Protein Data Bank (PDB; http://www.rcsb.org/pdb/) is the single worldwide archive of structural data of biological macromolecules.  ...  ACKNOWLEDGEMENTS The PDB would like to acknowledge the work of Dietmar Schomburg (Institute of Biochemistry at the University of Cologne), Project Leader of the BRENDA database for enzyme classification  ... 
doi:10.1093/nar/29.1.214 pmid:11125095 pmcid:PMC29799 fatcat:3osjvlwcsreprez4isx6fr27g4

The Protein Data Bank: unifying the archive

J. Westbrook
2002 Nucleic Acids Research  
We have now produced a collection of mmCIF data files for the PDB archive (ftp:// beta.rcsb.org/pub/pdb/uniformity/data/mmCIF/).  ...  This paper describes the progress that has been made in validating all data in the PDB archive and in releasing a uniform archive for the community.  ...  that have been contributed by colleagues at the NCBI, the EBI, the CCDC and the many users of the PDB.  ... 
doi:10.1093/nar/30.1.245 pmid:11752306 pmcid:PMC99110 fatcat:vgklfdq6bnagnhq2mox5p4p74e

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 wwPDB website at http://www.wwpdb. org/ provides information about services provided by the individual member organizations and about projects undertaken by the wwPDB.  ...  Funding to pay the Open Access publication charges for this article was provided by the agencies supporting the RCSB PDB.  ... 
doi:10.1093/nar/gkl971 pmid:17142228 pmcid:PMC1669775 fatcat:bukrvoz4dfdgda3vsb4df4rkgy

The Protein Data Bank

Helen M. Berman, Tammy Battistuz, T. N. Bhat, Wolfgang F. Bluhm, Philip E. Bourne, Kyle Burkhardt, Zukang Feng, Gary L. Gilliland, Lisa Iype, Shri Jain, Phoebe Fagan, Jessica Marvin (+7 others)
2002 Acta Crystallographica Section D: Biological Crystallography  
The Protein Data Bank [PDB; Berman, Westbrooket al.(2000),Nucleic Acids Res.28, 235–242; http://www.pdb.org/] is the single worldwide archive of primary structural data of biological macromolecules.  ...  This article describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource.  ...  The efforts of the entire PDB staff (listed at http:// www.rcsb.org/pdb/rcsb-group.html) are gratefully acknowledged.  ... 
doi:10.1107/s0907444902003451 pmid:12037327 fatcat:satbdpl4a5c2jk7uo42ovv2dgm

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  
examples taken from the recent depositions in PDB.  ...  These mosaic detectors are flatfield corrected in order to give a uniform response over the whole surface area.  ...  data in the Protein Data Bank (PDB) [3].  ... 
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  
examples taken from the recent depositions in PDB.  ...  These mosaic detectors are flatfield corrected in order to give a uniform response over the whole surface area.  ...  data in the Protein Data Bank (PDB) [3].  ... 
doi:10.1107/s0108767307099503 fatcat:owqaapy6cbd5hdtjpyxfvoukha

Is there a Sevres standard for protein structures?

A. Wlodawer, M. Jaskolski, Z. Dauter
2007 Acta Crystallographica Section A Foundations of Crystallography  
examples taken from the recent depositions in PDB.  ...  These mosaic detectors are flatfield corrected in order to give a uniform response over the whole surface area.  ...  data in the Protein Data Bank (PDB) [3].  ... 
doi:10.1107/s0108767307099527 fatcat:wi3y5qwpjjetppd75orkvadc5m

The distribution and query systems of the RCSB Protein Data Bank

P. E. Bourne
2004 Nucleic Acids Research  
The Protein Data Bank (PDB; http://www.pdb.org) is the primary source of information on the 3D structure of biological macromolecules.  ...  The PDB's mandate is to disseminate this information in the most usable form and as widely as possible.  ...  ACKNOWLEDGEMENTS The PDB is operated by Rutgers, The State University of New Jersey; the San Diego Supercomputer Center at the University of California, San Diego; and the Center for Advanced Research  ... 
doi:10.1093/nar/gkh096 pmid:14681399 pmcid:PMC308830 fatcat:o6qlkzgql5h6nf34lx4b67dbea

Mutual Information-Based Non-Local Total Variation Denoiser for Low-Dose Cone-Beam Computed Tomography

Ho Lee, Jiwon Sung, Yeonho Choi, Jun Won Kim, Ik Jae Lee
2021 Frontiers in Oncology  
The proposed method was evaluated using patient data and actual phantom measurement data acquired with lower mAs.  ...  In addition, achieving clinically acceptable CBCT image quality despite low-mAs projection acquisition can reduce the burden on common online CBCT imaging, improving patient safety throughout the course  ...  data and lower resolution projection data.  ... 
doi:10.3389/fonc.2021.751057 pmid:34745978 pmcid:PMC8567105 fatcat:476qa2kiqbeadir3fz3o6nlcsy

The wwPDB remediation project

G. J. Swaminathan, B. Schneider
2007 Acta Crystallographica Section A Foundations of Crystallography  
Data Bank (PDB) [3] .  ...  The wwPDB (http://www.wwpdb.org/) has collaborated on a project to remediate the PDB archive and create a new set of corrected files.  ... 
doi:10.1107/s0108767307099497 fatcat:jaobgr6wcrexnbd7kf3dnurv4q

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.  ...  This set the stage for the PDB to remain a single uniform global resource of structural biology data.  ... 
doi:10.1107/s0108767307035623 pmid:18156675 fatcat:75muama2a5fjne52mkampxpcpm

The Protein Data Bank

H. M. Berman
2000 Nucleic Acids Research  
The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules.  ...  This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.  ...  This has helped the PDB to continuously improve its procedures for producing entries. The cooperation of the BNL PDB staff is gratefully acknowledged.  ... 
doi:10.1093/nar/28.1.235 pmid:10592235 pmcid:PMC102472 fatcat:kbx7k4pmhjavrnogpn7xp7bn74

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

PyMine: a PyMOL plugin to integrate and visualize data for drug discovery

Rajan Chaudhari, Zhijun Li
2015 BMC Research Notes  
However, lack of integration makes it very challenging for individual scientists to access and understand all the data related to a specific protein of interest.  ...  of high-quality databases and presents them in a graphic and uniformed way.  ...  Research reported in this publication was supported in part by Grant Number UL1RR024134 from the National Center for Research Resources and in part by the Institute for Translational Medicine and Therapeutics  ... 
doi:10.1186/s13104-015-1483-3 pmid:26429562 pmcid:PMC4590260 fatcat:htrqquh7zvg5dcjelr5p5n5hxu

Deposition of diffraction images to be discussed at the Open Meeting of the Commission on Biological Macromolecules of the IUCr in Osaka

Edward Baker, Zbigniew Dauter, Mitchell Guss, Howard Einspahr
2008 Acta Crystallographica Section D: Biological Crystallography  
Today, all journals which publish macromolecular structures require that the refined coordinates be deposited in the Protein Data Bank (PDB). This is also demanded by most funding agencies.  ...  Deposition of coordinates is nowadays easy through the online systems provided by the PDB.  ...  Today, all journals which publish macromolecular structures require that the refined coordinates be deposited in the Protein Data Bank (PDB). This is also demanded by most funding agencies.  ... 
doi:10.1107/s0907444908004915 pmid:18391400 fatcat:gjzrwj3thvcjjca7rgegtoakty
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