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The Protein Data Bank: unifying the archive

J. Westbrook
2002 Nucleic Acids Research  
The Protein Data Bank (PDB; http://www.pdb.org/) is the single worldwide archive of structural data of biological macromolecules.  ...  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 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.  ...  INTRODUCTION Since 1971, 3D data for experimentally determined structures of proteins and nucleic acids have been deposited and archived in the Protein Data Bank (PDB). 1 Established at Brookhaven National  ... 
doi:10.1002/bip.22132 pmid:23023942 pmcid:PMC3684242 fatcat:tkdo6ykibnhebfbavqjb55nhsq

Impact Analysis of "Berman HM et al., (2000), The Protein Data Bank"

Jodi Basner
2017 RCSB Protein Data Bank  
macromolecules, The Protein Data Bank.  ...  macromolecules, The Protein Data Bank.  ...  Research Data Science & Evaluation Impact of the Protein Data Bank on the Research Community What is the Threshold for "Highly Cited"?  ... 
doi:10.2210/rcsb_pdb/pdb-cit-anal-2017 fatcat:odfaoxnry5bglb7eij5vhtcnwy

Analysis of impact metrics for the Protein Data Bank

Christopher Markosian, Luigi Di Costanzo, Monica Sekharan, Chenghua Shao, Stephen K. Burley, Christine Zardecki
2018 Scientific Data  
Since 1971, the Protein Data Bank (PDB) archive has served as the single, global repository for open access to atomic-level data for biological macromolecules.  ...  The archive currently holds >140,000 structures (>1 billion atoms). These structures are the molecules of life found in all organisms.  ...  We gratefully acknowledge contributions from all members of the Research Collaboratory for Structural Bioinformatics PDB, our Worldwide Protein Data Bank partners, and the Rutgers Office of Research Analytics  ... 
doi:10.1038/sdata.2018.212 pmid:30325351 pmcid:PMC6190746 fatcat:6o4xdmnaenadzbbsvgzekefwye

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

Protein Data Bank: the single global archive for 3D macromolecular structure data

Stephen K Burley, Helen M Berman, Charmi Bhikadiya, Chunxiao Bi, Li Chen, Luigi Di Costanzo, Cole Christie, Jose M Duarte, Shuchismita Dutta, Zukang Feng, Sutapa Ghosh, David S Goodsell (+70 others)
2018 Nucleic Acids Research  
The Protein Data Bank (PDB) is the single global archive of experimentally determined three-dimensional (3D) structure data of biological macromolecules.  ...  Since 2003, the PDB has been managed by the Worldwide Protein Data Bank (wwPDB; wwpdb.org), an international consortium that collaboratively oversees deposition, validation, biocuration, and open access  ...  ; rcsb. org) (3), the Protein Data Bank in Europe (PDBe; pdbe. org) (4), Protein Data Bank Japan (PDBj; pdbj.org) (5) and BioMagResBank (BMRB; www.bmrb.wisc.edu) (6) .  ... 
doi:10.1093/nar/gky949 pmid:30357364 pmcid:PMC6324056 fatcat:ca3xenxsdzgvnb7vcwi2gtomoa

Activities of PDBj and wwPDB : A new PDB format, Data Deposition, Validation, and Data Integration(PDBj: Protein Data Bank Japan,The 51st Annual Meeting of the Biophysical Society of Japan)

Haruki Nakamura
2013 Seibutsu Butsuri  
The Protein Data Bank Japan (PDBj, http://pdbj.org) is a member of the worldwide Protein Data Bank (wwPDB, http://wwpdbj.org/) and accepts and processes the deposited data of experimentally determined  ...  While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins, which are summarized  ...  To enhance the interoperability of the BMRB archival data in addition to the NMR-STAR format, the PDBj-BMRB began to provide the data in standard structured data formats, which are an Extensible Markup  ... 
doi:10.2142/biophys.53.s286_1 fatcat:5bl4c43nubeajjjpewlmpuavve

PDBj-BMRB : Publishing NMR Spectroscopy Derived Data of BioMagResBank in Structured Data Formats, XML and RDF(PDBj: Protein Data Bank Japan,The 51st Annual Meeting of the Biophysical Society of Japan)

Masashi Yokochi
2013 Seibutsu Butsuri  
The Protein Data Bank Japan (PDBj, http://pdbj.org) is a member of the worldwide Protein Data Bank (wwPDB, http://wwpdbj.org/) and accepts and processes the deposited data of experimentally determined  ...  While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins, which are summarized  ...  To enhance the interoperability of the BMRB archival data in addition to the NMR-STAR format, the PDBj-BMRB began to provide the data in standard structured data formats, which are an Extensible Markup  ... 
doi:10.2142/biophys.53.s286_3 fatcat:gs5cgv4akrfxriqsubclnvz6hy

The new PDBj web Interface : Customizable, Modern and User-friendly(PDBj: Protein Data Bank Japan,The 51st Annual Meeting of the Biophysical Society of Japan)

Gert-Jan Bekker
2013 Seibutsu Butsuri  
The Protein Data Bank Japan (PDBj, http://pdbj.org) is a member of the worldwide Protein Data Bank (wwPDB, http://wwpdbj.org/) and accepts and processes the deposited data of experimentally determined  ...  While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins, which are summarized  ...  To enhance the interoperability of the BMRB archival data in addition to the NMR-STAR format, the PDBj-BMRB began to provide the data in standard structured data formats, which are an Extensible Markup  ... 
doi:10.2142/biophys.53.s286_2 fatcat:jwa4gpvwu5bwxbkuytbjfsptxm

OneDep: unified wwPDB system for deposition, biocuration and validation of macromolecular structures in the PDB archive

Jasmine Y. Young, John Westbrook, Zukang Feng, wwPDB Biocuration Team, wwPDB Onedep Team, John Markley, Haruki Nakamura, Sameer Velankar, Stephen K. Burley
2017 Acta Crystallographica Section A: Foundations and Advances  
The Protein Data Bank (PDB) is the single global repository for three-dimensional structures of biological macromolecules and their complexes.  ...  There are more than 590 millions data file downloads from the PDB archive and more than 1 million unique IP addresses access the archive every year.  ...  The Protein Data Bank (PDB) is the single global repository for three-dimensional structures of biological macromolecules and their complexes.  ... 
doi:10.1107/s0108767317099536 fatcat:ml7nsvdj4nfsxhbs4evta3vgga

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  
OneDep unifies deposition, biocuration, and validation pipelines across all wwPDB, EMDB, and BMRB deposition sites with improved focus on data quality and completeness in these archives, while supporting  ...  OneDep, a unified system for deposition, biocuration, and validation of experimentally determined structures of biological macromolecules to the PDB archive, has been developed as a global collaboration  ...  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

Atypical structural tendencies among low-complexity domains in the protein data bank proteome

Sean M. Cascarina, Mikaela R. Elder, Eric D. Ross, Björn Wallner
2020 PLoS Computational Biology  
A variety of studies have suggested that low-complexity domains (LCDs) tend to be intrinsically disordered and are relatively rare within structured proteins in the Protein Data Bank (PDB).  ...  Secondary structure tendencies varied as a function of the identity of the amino acid enriched and its degree of enrichment.  ...  Methods Data acquisition and processing Protein sequences as well as corresponding secondary structure and intrinsic disorder annotations for all protein chains found in the Protein Data Bank (PDB) were  ... 
doi:10.1371/journal.pcbi.1007487 pmid:31986130 fatcat:7ozzoxgcx5bwlo7kg5n63g4vfq

Gammasphaerolipovirus, a newly proposed bacteriophage genus, unifies viruses of halophilic archaea and thermophilic bacteria within the novel family Sphaerolipoviridae

Alice Pawlowski, Ilona Rissanen, Jaana K. H. Bamford, Mart Krupovic, Matti Jalasvuori
2014 Archives of Virology  
It comprises icosahedral, tailless haloarchaeal viruses with an internal lipid membrane located between the protein capsid and the dsDNA genome.  ...  Alpha-and betasphaerolipoviruses share with P23-77-like bacteriophages a conserved block of core genes that encode a putative genome-packaging ATPase and the two major capsid proteins (MCPs).  ...  Thus, core proteins may serve as signature sequences for the identification of putative new members of the three genera in future data bank searches.  ... 
doi:10.1007/s00705-013-1970-6 pmid:24395078 fatcat:jkdu5hc6cnbarl2dx6knjrjvyi

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  
Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data.  ...  Abstract The Protein Data Bank (PDB) is the single global repository for experimentally determined 3D structures of biological macromolecules and their complexes with ligands.  ...  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

PDBe: Protein Data Bank in Europe

S. Velankar, C. Best, B. Beuth, C. H. Boutselakis, N. Cobley, A. W. Sousa Da Silva, D. Dimitropoulos, A. Golovin, M. Hirshberg, M. John, E. B. Krissinel, R. Newman (+13 others)
2009 Nucleic Acids Research  
The Protein Data Bank in Europe (PDBe) (http://www .ebi.ac.uk/pdbe/) is actively working with its Worldwide Protein Data Bank partners to enhance the quality and consistency of the international archive  ...  of bio-macromolecular structure data, the Protein Data Bank (PDB).  ...  ACKNOWLEDGEMENTS We wish to thank all collaborators and partners in the EBI, EMBL, wwPDB and other collaborative efforts, as  ... 
doi:10.1093/nar/gkp916 pmid:19858099 pmcid:PMC2808887 fatcat:amgz3equ6jgenhym77vbghy47e
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