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The Protein Data Bank: unifying the archive
2002
Nucleic Acids Research
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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
2012
Biopolymers
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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"
2017
RCSB Protein Data Bank
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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
2018
Scientific Data
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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
2004
Nucleic Acids Research
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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
2018
Nucleic Acids Research
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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)
2013
Seibutsu Butsuri
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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)
2013
Seibutsu Butsuri
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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)
2013
Seibutsu Butsuri
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The file type is application/pdf.
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
2017
Acta Crystallographica Section A: Foundations and Advances
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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
2017
Structure
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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
2020
PLoS Computational Biology
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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
2014
Archives of Virology
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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
2018
Database: The Journal of Biological Databases and Curation
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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
2009
Nucleic Acids Research
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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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